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/7774412/working' mkdir: created directory `/scratch/stefan/7774412/working/protonate' Storing results in /scratch/stefan/7774412/finished Working in /scratch/stefan/7774412/working /scratch/stefan/7774412/working /scratch/stefan/7774412 /scratch/stefan/7774412/working/protonate /scratch/stefan/7774412/working /scratch/stefan/7774412 Precomputing protomers for all compounds (pH: 7.4) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1575 protomers created Coalesing and merging protomers 1251 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1269 protomers after new stereo-center expansion /scratch/stefan/7774412/working /scratch/stefan/7774412 Bulk generating 3D conformations all protomers in /scratch/stefan/7774412/working/3D mkdir: created directory `/scratch/stefan/7774412/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7774412/working/protonate/xaaaadj-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' 1270 3D conformations generated for 1000 compounds Building REAL300004087001 mkdir: created directory `/scratch/stefan/7774412/working/building' mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087001' /scratch/stefan/7774412/working/building/REAL300004087001 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087001 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087001/0 /scratch/stefan/7774412/working/building/REAL300004087001 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1 `/scratch/stefan/7774412/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1) `REAL300004087001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087001 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 12, 12, 5, 3, 3, 1, 3, 1, 1, 6, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 6, 6, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 46, 44, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087001 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 5, 11, 19, 19, 19, 19, 19, 19, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 11, 11, 19, 19, 19, 19, 5, 5, 5, 5, 5, 5, 5, 5] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087001 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 36, 36, 36, 19, 11, 11, 9, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 36, 36, 11, 3, 3, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 152 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087001 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087001/1 /scratch/stefan/7774412/working/building/REAL300004087001 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/2 `/scratch/stefan/7774412/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1) `REAL300004087001.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087001 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 107, 113, 113, 80, 17, 5, 1, 5, 1, 1, 8, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 80, 80, 80, 80, 107, 107, 8, 8, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 38, 39, 40, 41, 10, 43, 12, 13, 44, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087001 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 49, 49, 80, 123, 165, 165, 165, 165, 165, 165, 80, 80, 80, 80, 80, 1, 2, 2, 2, 2, 2, 123, 123, 165, 165, 165, 165, 80, 80, 80, 80, 80, 80, 80, 80] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087001 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=CC(F)=C3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 201, 201, 201, 165, 69, 21, 15, 21, 3, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 165, 165, 165, 165, 201, 201, 3, 3, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 480 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087001 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087001 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `/scratch/stefan/7774412/finished' Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087001/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087001/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087001 Building REAL300004087002 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087002' /scratch/stefan/7774412/working/building/REAL300004087002 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087002 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087002/0 /scratch/stefan/7774412/working/building/REAL300004087002 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/3 `/scratch/stefan/7774412/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=CC(OC(C)(C)C)=N2)S1) `REAL300004087002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087002 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=CC(OC(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 16, 22, 22, 13, 13, 13, 9, 13, 5, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 1, 13, 13, 13, 13, 16, 16, 13, 9, 9, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6] 31 rigid atoms, others: [36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087002 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=CC(OC(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 9, 13, 13, 13, 13, 13, 24, 26, 26, 26, 13, 1, 2, 2, 2, 2, 2, 2, 7, 7, 9, 9, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087002 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087002 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087002/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087002 Building REAL300004087003 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087003' /scratch/stefan/7774412/working/building/REAL300004087003 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087003 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087003/0 /scratch/stefan/7774412/working/building/REAL300004087003 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/4 `/scratch/stefan/7774412/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C2=CC=CC=C2)S1) `REAL300004087003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087003 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 8, 8, 8, 8, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3] 15 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087003 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 47 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087003 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 6, 5, 3, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 6, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 15 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087003 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087003/1 /scratch/stefan/7774412/working/building/REAL300004087003 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/5 `/scratch/stefan/7774412/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCN2C2=CC=CC=C2)S1) `REAL300004087003.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087003 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 73, 73, 73, 56, 15, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 56, 56, 56, 56, 73, 73, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3] 73 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40]) total number of confs: 186 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087003 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 43, 43, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 2, 2, 2, 2, 2, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087003 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCN2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 73, 73, 73, 56, 15, 5, 3, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 73, 73, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 73 rigid atoms, others: [36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 179 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087003 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087003 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087003/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087003/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087003 Building REAL300004087004 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087004' /scratch/stefan/7774412/working/building/REAL300004087004 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087004 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087004/0 /scratch/stefan/7774412/working/building/REAL300004087004 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/6 `/scratch/stefan/7774412/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC(NC2CC2)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087004 none CC1=NSC(NC2CC2)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 8, 5, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 8, 1, 1, 1, 1, 19, 19, 32, 32, 39, 61, 61, 61, 106, 106, 106, 61, 61, 61, 19, 19, 19, 8, 1, 1, 1, 1, 1, 39, 106, 106, 61, 61, 61] 106 rigid atoms, others: [5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087004 none CC1=NSC(NC2CC2)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 8, 5, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 19, 19, 1, 1, 8, 8, 10, 19, 19, 19, 37, 68, 68, 18, 18, 18, 2, 2, 2, 10, 19, 19, 19, 19, 19, 10, 37, 37, 19, 19, 19] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10] set([6, 7, 8, 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: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087004 none CC1=NSC(NC2CC2)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 8, 5, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [19, 18, 18, 18, 18, 19, 37, 62, 62, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 19, 19, 19, 37, 62, 62, 62, 62, 62, 2, 2, 2, 2, 2, 2] 106 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087004 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087004 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087004/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087004 Building REAL300004087005 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087005' /scratch/stefan/7774412/working/building/REAL300004087005 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087005 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087005/0 /scratch/stefan/7774412/working/building/REAL300004087005 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/7 `/scratch/stefan/7774412/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC2=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C(C)N=C21) `REAL300004087005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087005 none CCN1N=CC2=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C(C)N=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [25, 14, 14, 14, 14, 14, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 14, 14, 14, 25, 25, 25, 25, 25, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14] 45 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087005 none CCN1N=CC2=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C(C)N=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 14, 14, 14, 27, 31, 31, 14, 14, 14, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 12, 27, 27, 14, 14, 14, 2, 2, 2] 45 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087005 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087005 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087005/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087005 Building REAL300004087006 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087006' /scratch/stefan/7774412/working/building/REAL300004087006 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087006 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087006/0 /scratch/stefan/7774412/working/building/REAL300004087006 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/8 `/scratch/stefan/7774412/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=CC=N2)S1) `REAL300004087006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087006 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 40, 63, 63, 21, 16, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 21, 22, 22, 22, 40, 40, 16, 1, 1, 12, 12, 12, 12] 98 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) 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: REAL300004087006 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 21, 21, 21, 21, 21, 66, 66, 66, 66, 66, 1, 2, 2, 2, 2, 2, 2, 21, 21, 66, 66, 66, 66] 98 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087006 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 98, 98, 98, 66, 60, 54, 12, 54, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 98, 98, 60, 12, 12, 1, 1, 1, 1] 98 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 345 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087006 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087006 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087006/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087006 Building REAL300004087007 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087007' /scratch/stefan/7774412/working/building/REAL300004087007 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087007 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087007/0 /scratch/stefan/7774412/working/building/REAL300004087007 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/9 `/scratch/stefan/7774412/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3)N=CO2)S1) `REAL300004087007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087007 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3)N=CO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 55, 85, 85, 29, 17, 13, 1, 13, 1, 1, 1, 7, 7, 2, 7, 7, 1, 1, 1, 29, 29, 29, 29, 55, 55, 17, 7, 7, 2, 7, 7, 1] 87 rigid atoms, others: [35, 10, 12, 13, 14, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087007 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3)N=CO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 29, 29, 51, 51, 42, 51, 51, 29, 29, 29, 1, 2, 2, 2, 2, 2, 2, 51, 51, 47, 51, 51, 29] 87 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087007 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3)N=CO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 87, 87, 87, 51, 38, 30, 7, 30, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 51, 51, 51, 51, 87, 87, 38, 1, 1, 1, 1, 1, 7] 87 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 340 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087007 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087007 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087007/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087007 Building REAL300004087008 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087008' /scratch/stefan/7774412/working/building/REAL300004087008 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087008 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087008/0 /scratch/stefan/7774412/working/building/REAL300004087008 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/10 `/scratch/stefan/7774412/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(O)(C3=CC=CC(Cl)=C3)C2)S1) `REAL300004087008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087008 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(O)(C3=CC=CC(Cl)=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 7, 10, 10, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 3, 9, 9, 9, 1, 5, 5, 5, 5, 7, 7, 5, 1, 1, 1, 6, 9, 9, 8, 9, 1, 1] 66 rigid atoms, others: [32, 33, 39, 40, 10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087008 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(O)(C3=CC=CC(Cl)=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 15, 14, 15, 15, 15, 5, 1, 2, 2, 2, 3, 3, 2, 5, 5, 5, 15, 15, 15, 15, 15, 5, 5] 66 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087008 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(O)(C3=CC=CC(Cl)=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 1, 16, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 22, 22, 22, 15, 15, 13, 9, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 22, 22, 15, 9, 9, 9, 27, 1, 1, 1, 1, 9, 9] 66 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40]) total number of confs: 108 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087008 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087008 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087008/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087008 Building REAL300004087009 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087009' /scratch/stefan/7774412/working/building/REAL300004087009 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087009 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087009/0 /scratch/stefan/7774412/working/building/REAL300004087009 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/11 `/scratch/stefan/7774412/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=CC(C(F)F)=N2)S1) `REAL300004087009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087009 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=CC(C(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 5, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 7, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 1, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 1, 4] 9 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087009 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=CC(C(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 5, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 5, 5, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087009 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087009/1 /scratch/stefan/7774412/working/building/REAL300004087009 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/12 `/scratch/stefan/7774412/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=CC(C(F)F)=N2)S1) `REAL300004087009.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087009/1/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: REAL300004087009 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=CC(C(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 5, 15, 15, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 11, 9, 6, 9, 1, 1, 1, 1, 1, 1, 8, 8, 1, 21, 21, 21, 21, 21, 21, 6, 6, 1, 1, 8] 21 rigid atoms, others: [12, 13, 14, 15, 16, 17, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087009 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=CC(C(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 5, 15, 15, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087009 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087009 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087009/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087009/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087009 Building REAL300004087010 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087010' /scratch/stefan/7774412/working/building/REAL300004087010 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087010 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087010/0 /scratch/stefan/7774412/working/building/REAL300004087010 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/13 `/scratch/stefan/7774412/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2N=NN=C2C(C)(C)C)S1) `REAL300004087010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087010 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2N=NN=C2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 8, 8, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 24, 24, 24, 15, 12, 11, 2, 11, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 24, 24, 11, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2] 24 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087010 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2N=NN=C2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 8, 8, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 14, 14, 14, 14, 14, 15, 14, 15, 1, 2, 2, 2, 2, 2, 2, 13, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087010 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087010/1 /scratch/stefan/7774412/working/building/REAL300004087010 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/14 `/scratch/stefan/7774412/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)N2N=NN=C2C(C)(C)C)S1) `REAL300004087010.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087010/1/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: REAL300004087010 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)N2N=NN=C2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 8, 8, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 72, 72, 72, 58, 23, 10, 2, 10, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 72, 72, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 72 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087010 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)N2N=NN=C2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 8, 8, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 38, 38, 51, 51, 58, 58, 58, 58, 58, 58, 58, 58, 1, 2, 2, 2, 2, 2, 51, 51, 51, 51, 58, 58, 58, 58, 58, 58, 58, 58, 58] 72 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087010 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087010 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087010/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087010/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087010 Building REAL300004087011 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087011' /scratch/stefan/7774412/working/building/REAL300004087011 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087011 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087011/0 /scratch/stefan/7774412/working/building/REAL300004087011 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/15 `/scratch/stefan/7774412/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN(C)C=C2)S1) `REAL300004087011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087011 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 26, 26, 26, 21, 21, 21, 7, 20, 7, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 26, 26, 21, 7, 7, 1, 2, 2, 2, 1, 1] 26 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087011 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 11, 11, 21, 21, 21, 21, 21, 1, 2, 2, 2, 3, 3, 2, 11, 11, 21, 21, 21, 21, 21, 21] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087011 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087011 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087011/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087011 Building REAL300004087012 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087012' /scratch/stefan/7774412/working/building/REAL300004087012 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087012 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087012/0 /scratch/stefan/7774412/working/building/REAL300004087012 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/16 `/scratch/stefan/7774412/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC3=CC=CC=C3S2)S1) `REAL300004087012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087012 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 23, 23, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 22, 22, 8, 1, 1, 1, 1] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087012 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 13, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087012 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087012 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087012/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087012 Building REAL300004087013 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087013' /scratch/stefan/7774412/working/building/REAL300004087013 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087013 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087013/0 /scratch/stefan/7774412/working/building/REAL300004087013 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/17 `/scratch/stefan/7774412/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1) `REAL300004087013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087013 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 39, 41, 41, 24, 24, 23, 7, 24, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 1, 1, 24, 24, 24, 24, 39, 39, 24, 7, 7, 5, 5, 5, 5, 1] 55 rigid atoms, others: [38, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087013 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 39, 39, 34, 39, 39, 39, 24, 24, 1, 2, 2, 2, 2, 2, 2, 12, 12, 39, 39, 39, 39, 24] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087013 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 55, 55, 55, 39, 39, 39, 21, 39, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 39, 39, 39, 39, 55, 55, 39, 21, 21, 1, 1, 1, 1, 5] 55 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087013 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087013/1 /scratch/stefan/7774412/working/building/REAL300004087013 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/18 `/scratch/stefan/7774412/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1) `REAL300004087013.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087013 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 156, 156, 156, 118, 58, 27, 6, 28, 1, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 1, 1, 118, 118, 118, 118, 156, 156, 6, 6, 6, 6, 6, 6, 1] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087013 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 27, 27, 68, 118, 118, 118, 175, 175, 118, 118, 175, 175, 118, 118, 1, 2, 2, 2, 2, 2, 68, 68, 175, 175, 175, 175, 118] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 583 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087013 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 201, 201, 201, 175, 120, 73, 22, 74, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 175, 175, 175, 175, 201, 201, 22, 22, 1, 1, 1, 1, 6] 201 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 539 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087013 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087013 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087013/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087013/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087013 Building REAL300004087014 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087014' /scratch/stefan/7774412/working/building/REAL300004087014 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087014 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087014/0 /scratch/stefan/7774412/working/building/REAL300004087014 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/19 `/scratch/stefan/7774412/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC3=CC=CC=C32)S1) `REAL300004087014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087014 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 11, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 11, 7, 7, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087014 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 4, 4, 11, 11, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087014 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087014/1 /scratch/stefan/7774412/working/building/REAL300004087014 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/20 `/scratch/stefan/7774412/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC3=CC=CC=C32)S1) `REAL300004087014.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087014/1/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: REAL300004087014 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 201, 201, 201, 157, 88, 39, 8, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 201, 201, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087014 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 31, 31, 92, 157, 157, 157, 157, 157, 157, 157, 157, 1, 2, 2, 2, 2, 2, 92, 92, 157, 157, 157, 157, 157] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087014 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087014 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087014/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087014/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087014 Building REAL300004087015 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087015' /scratch/stefan/7774412/working/building/REAL300004087015 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087015 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087015/0 /scratch/stefan/7774412/working/building/REAL300004087015 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/21 `/scratch/stefan/7774412/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC2=CC=CC=C2N1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087015 none CCC1=NC2=CC=CC=C2N1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 9, 9, 9, 9, 4, 4, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087015 none CCC1=NC2=CC=CC=C2N1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 15, 19, 19, 9, 9, 9, 5, 5, 5, 4, 4, 1, 1, 1, 1, 5, 5, 9, 15, 15, 9, 9, 9] 27 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087015 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087015/1 /scratch/stefan/7774412/working/building/REAL300004087015 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/22 `/scratch/stefan/7774412/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC2=CC=CC=C2N1CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087015.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087015/1/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: REAL300004087015 none CCC1=NC2=CC=CC=C2N1CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 113, 113, 113, 113, 113, 113, 113, 113, 113, 62, 26, 10, 26, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 167, 167, 167, 167, 167, 113, 113, 113, 113, 62, 62, 2, 2, 2, 2, 2] 201 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 648 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087015 none CCC1=NC2=CC=CC=C2N1CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 22, 22, 46, 113, 113, 113, 159, 182, 182, 113, 113, 113, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 159, 159, 113, 113, 113] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 30, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087015 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087015 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087015/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087015/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087015 Building REAL300004087016 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087016' /scratch/stefan/7774412/working/building/REAL300004087016 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087016 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087016/0 /scratch/stefan/7774412/working/building/REAL300004087016 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/23 `/scratch/stefan/7774412/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(NS(C)(=O)=O)C(C)C)S1) `REAL300004087016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087016 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(NS(C)(=O)=O)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 14, 5, 11, 11, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087016 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087016/1 /scratch/stefan/7774412/working/building/REAL300004087016 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/24 `/scratch/stefan/7774412/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(NS(C)(=O)=O)C(C)C)S1) `REAL300004087016.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087016 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(NS(C)(=O)=O)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 14, 5, 11, 11, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 1, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087016 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087016 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087016/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087016/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087016 Building REAL300004087017 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087017' /scratch/stefan/7774412/working/building/REAL300004087017 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087017 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087017/0 /scratch/stefan/7774412/working/building/REAL300004087017 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/25 `/scratch/stefan/7774412/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2CCC3=CC=CC=C32)S1) `REAL300004087017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087017 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 49, 49, 49, 29, 20, 19, 7, 19, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 49, 49, 20, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 198 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087017 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 29, 29, 29, 29, 29, 29, 29, 29] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087017 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087017/1 /scratch/stefan/7774412/working/building/REAL300004087017 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/26 `/scratch/stefan/7774412/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)N2CCC3=CC=CC=C32)S1) `REAL300004087017.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087017/1/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: REAL300004087017 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)N2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 168, 168, 168, 132, 47, 13, 6, 13, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 168, 168, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 168 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 413 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: REAL300004087017 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)N2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 68, 68, 107, 107, 132, 132, 132, 132, 132, 132, 132, 132, 1, 2, 2, 2, 2, 2, 107, 107, 107, 107, 132, 132, 132, 132, 132, 132, 132, 132] 168 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 427 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087017 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087017 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087017/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087017/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087017 Building REAL300004087018 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087018' /scratch/stefan/7774412/working/building/REAL300004087018 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087018 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087018/0 /scratch/stefan/7774412/working/building/REAL300004087018 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/27 `/scratch/stefan/7774412/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=NN=C3)N(C)N=C2)S1) `REAL300004087018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087018 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=NN=C3)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 2, 2, 2, 1] 5 rigid atoms, others: [35, 10, 12, 13, 14, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 18 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087018 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=NN=C3)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 5, 5, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 5, 5, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087018 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=NN=C3)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 8, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 6 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087018 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087018 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087018/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087018 Building REAL300004087019 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087019' /scratch/stefan/7774412/working/building/REAL300004087019 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087019 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087019/0 /scratch/stefan/7774412/working/building/REAL300004087019 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/28 `/scratch/stefan/7774412/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=NN=C2)S1) `REAL300004087019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087019 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=NN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 3, 1, 2, 2, 2, 1, 1, 3, 3] 5 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087019 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=NN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087019 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=NN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 2, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 1, 1] 5 rigid atoms, others: [37, 38, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 25 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087019 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087019 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087019/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087019 Building REAL300004087020 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087020' /scratch/stefan/7774412/working/building/REAL300004087020 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087020 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087020/0 /scratch/stefan/7774412/working/building/REAL300004087020 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/29 `/scratch/stefan/7774412/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC(N(C)C)=NO2)S1) `REAL300004087020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087020 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC(N(C)C)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 1, 8, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 72, 72, 72, 43, 43, 41, 23, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 72, 72, 43, 23, 23, 9, 9, 2, 2, 2, 2, 2, 2] 72 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087020 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC(N(C)C)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 1, 8, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 8, 16, 43, 43, 43, 43, 43, 43, 43, 1, 2, 2, 2, 3, 3, 2, 8, 8, 16, 16, 43, 43, 43, 43, 43, 43] 72 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087020 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087020 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087020/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087020 Building REAL300004087021 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087021' /scratch/stefan/7774412/working/building/REAL300004087021 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087021 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087021/0 /scratch/stefan/7774412/working/building/REAL300004087021 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/30 `/scratch/stefan/7774412/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=CC=CC=N2)S1) `REAL300004087021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087021 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 97, 97, 97, 75, 55, 55, 13, 55, 1, 13, 13, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 97, 97, 55, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 97 rigid atoms, others: [34, 35, 36, 37, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087021 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 21, 21, 21, 75, 75, 75, 75, 75, 1, 2, 2, 2, 2, 2, 2, 21, 21, 21, 22, 22, 22, 75, 75, 75, 75] 97 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087021 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087021/1 /scratch/stefan/7774412/working/building/REAL300004087021 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/31 `/scratch/stefan/7774412/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=CC=CC=N2)S1) `REAL300004087021.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087021/1/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: REAL300004087021 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 57, 57, 57, 53, 37, 31, 7, 31, 1, 7, 7, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 57, 57, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 57 rigid atoms, others: [33, 34, 35, 36, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087021 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 13, 13, 39, 39, 39, 53, 53, 53, 53, 53, 1, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 53, 53, 53, 53] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087021 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087021 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087021/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087021/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087021 Building REAL300004087022 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087022' /scratch/stefan/7774412/working/building/REAL300004087022 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087022 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087022/0 /scratch/stefan/7774412/working/building/REAL300004087022 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/32 `/scratch/stefan/7774412/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NN2C)S1) `REAL300004087022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087022 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 15, 17, 17, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 10, 15, 15, 10, 1, 1, 6, 6, 6, 6, 6] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087022 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 3, 10, 10, 19, 19, 19, 19, 19] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087022 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 25, 25, 25, 19, 19, 17, 6, 17, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 25, 25, 19, 6, 6, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 33, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087022 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087022 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087022/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087022 Building REAL300004087023 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087023' /scratch/stefan/7774412/working/building/REAL300004087023 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087023 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087023/0 /scratch/stefan/7774412/working/building/REAL300004087023 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/33 `/scratch/stefan/7774412/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CSCC2=CC=C(C(C)(C)C)C=C2)S1) `REAL300004087023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087023 none CC1=C(CC(=O)[O-])N=C(NC(=O)CSCC2=CC=C(C(C)(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 156, 201, 201, 106, 106, 106, 88, 106, 21, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 106, 106, 106, 106, 156, 156, 106, 88, 88, 3, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 201 rigid atoms, others: [48, 36, 37, 14, 15, 16, 17, 18, 19, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 847 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087023 none CC1=C(CC(=O)[O-])N=C(NC(=O)CSCC2=CC=C(C(C)(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 12, 22, 72, 106, 106, 90, 106, 146, 146, 146, 106, 106, 1, 2, 2, 2, 2, 2, 2, 12, 12, 72, 72, 106, 106, 146, 146, 146, 146, 146, 146, 146, 146, 146, 106, 106] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087023 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087023/1 /scratch/stefan/7774412/working/building/REAL300004087023 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/34 `/scratch/stefan/7774412/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSCC2=CC=C(C(C)(C)C)C=C2)S1) `REAL300004087023.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087023/1/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: REAL300004087023 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSCC2=CC=C(C(C)(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 179, 201, 201, 163, 92, 37, 13, 37, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 163, 163, 163, 163, 179, 179, 13, 13, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087023 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSCC2=CC=C(C(C)(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 11, 35, 35, 75, 106, 162, 162, 162, 162, 162, 184, 184, 184, 162, 162, 1, 2, 2, 2, 2, 2, 75, 75, 162, 162, 162, 162, 184, 184, 184, 184, 184, 184, 184, 184, 184, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087023 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087023 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087023/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087023/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087023 Building REAL300004087024 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087024' /scratch/stefan/7774412/working/building/REAL300004087024 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087024 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087024/0 /scratch/stefan/7774412/working/building/REAL300004087024 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/35 `/scratch/stefan/7774412/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=C3)=CC=N2)S1) `REAL300004087024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087024 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=C3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 30, 47, 47, 16, 13, 9, 1, 9, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 16, 17, 17, 17, 30, 30, 13, 1, 3, 3, 2, 3, 3, 1, 1] 47 rigid atoms, others: [37, 38, 10, 12, 13, 14, 15, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087024 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=C3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 29, 29, 16, 29, 29, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 29, 29, 17, 29, 29, 16, 16] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087024 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=C3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 47, 47, 47, 29, 23, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 29, 29, 29, 29, 47, 47, 23, 3, 1, 1, 1, 1, 1, 3, 3] 47 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 176 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087024 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087024 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087024/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087024 Building REAL300004087025 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087025' /scratch/stefan/7774412/working/building/REAL300004087025 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087025 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087025/0 /scratch/stefan/7774412/working/building/REAL300004087025 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/36 `/scratch/stefan/7774412/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CN3C=N2)S1) `REAL300004087025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087025 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CN3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 9, 9, 9, 17, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 8, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087025 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CN3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 8, 8, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087025 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087025 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087025/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087025 Building REAL300004087026 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087026' /scratch/stefan/7774412/working/building/REAL300004087026 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087026 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087026/0 /scratch/stefan/7774412/working/building/REAL300004087026 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/37 `/scratch/stefan/7774412/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC=C2)S1) `REAL300004087026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087026 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 54, 54, 54, 34, 23, 20, 4, 20, 1, 4, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 54, 54, 23, 4, 12, 1, 1, 1, 1, 1] 162 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087026 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 23, 23, 34, 34, 25, 34, 34, 1, 2, 2, 2, 2, 2, 2, 23, 69, 34, 34, 34, 34, 34] 162 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087026 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087026/1 /scratch/stefan/7774412/working/building/REAL300004087026 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/38 `/scratch/stefan/7774412/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC=C2)S1) `REAL300004087026.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087026/1/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: REAL300004087026 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 201, 201, 201, 154, 59, 17, 4, 17, 1, 4, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 201, 201, 4, 12, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087026 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 54, 54, 123, 123, 154, 154, 137, 154, 154, 1, 2, 2, 2, 2, 2, 123, 369, 154, 154, 154, 154, 154] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 971 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087026 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087026 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087026/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087026/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087026 Building REAL300004087027 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087027' /scratch/stefan/7774412/working/building/REAL300004087027 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087027 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087027/0 /scratch/stefan/7774412/working/building/REAL300004087027 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/39 `/scratch/stefan/7774412/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087027 none CCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 6, 17, 36, 6, 6, 6, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6] 73 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 240 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087027 none CCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 7, 15, 1, 1, 1, 1, 1, 5, 5, 6, 8, 8, 8, 15, 39, 39, 8, 8, 8, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 6, 15, 15, 8, 8, 8, 1, 1] 115 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 42, 43, 2, 22, 23] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 223 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087027 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087027 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087027/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087027 Building REAL300004087028 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087028' /scratch/stefan/7774412/working/building/REAL300004087028 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087028 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087028/0 /scratch/stefan/7774412/working/building/REAL300004087028 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/40 `/scratch/stefan/7774412/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N(C)C)=C2)S1) `REAL300004087028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087028 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1] 39 rigid atoms, others: [37, 10, 12, 13, 14, 15, 16, 17, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087028 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 21, 21, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 21, 21, 21, 21, 21, 21, 13] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087028 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087028 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087028/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087028 Building REAL300004087029 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087029' /scratch/stefan/7774412/working/building/REAL300004087029 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087029 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087029/0 /scratch/stefan/7774412/working/building/REAL300004087029 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/41 `/scratch/stefan/7774412/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087029 none CNC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 19, 10, 19, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 25, 25, 25, 25, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2] 43 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 116 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087029 none CNC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 37, 43, 43, 19, 19, 19, 8, 8, 8, 8, 1, 1, 1, 1, 11, 37, 37, 19, 19, 19] 43 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087029 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087029 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087029/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087029 Building REAL300004087030 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087030' /scratch/stefan/7774412/working/building/REAL300004087030 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087030 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087030/0 /scratch/stefan/7774412/working/building/REAL300004087030 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/42 `/scratch/stefan/7774412/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=C2O)S1) `REAL300004087030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087030 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=C2O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 43, 43, 43, 27, 27, 27, 27, 27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 43, 43, 27, 27, 27, 1, 1, 1, 1, 2] 86 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 178 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087030 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=C2O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 5, 14, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 3, 3, 2, 5, 5, 27, 27, 27, 27, 54] 86 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 129 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087030 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087030/1 /scratch/stefan/7774412/working/building/REAL300004087030 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/43 `/scratch/stefan/7774412/working/3D/43' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=C2O)S1) `REAL300004087030.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087030/1/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: REAL300004087030 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=C2O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 201, 201, 201, 184, 135, 90, 37, 90, 11, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 201, 201, 37, 37, 1, 1, 1, 1, 2] 402 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 531 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087030 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=C2O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 28, 28, 58, 142, 184, 184, 159, 184, 184, 184, 1, 2, 2, 2, 2, 2, 58, 58, 184, 184, 184, 184, 368] 402 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 894 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087030 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087030 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087030/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087030/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087030 Building REAL300004087031 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087031' /scratch/stefan/7774412/working/building/REAL300004087031 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087031 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087031/0 /scratch/stefan/7774412/working/building/REAL300004087031 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/44 `/scratch/stefan/7774412/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC2=CC=CC=C2C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C) `REAL300004087031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087031 none CCC1=NC2=CC=CC=C2C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 10, 10, 10, 11, 11, 11, 11, 10, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 11, 19, 19, 19, 19, 19, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11] 25 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087031 none CCC1=NC2=CC=CC=C2C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 11, 11, 11, 21, 23, 23, 10, 10, 10, 1, 1, 4, 4, 4, 3, 3, 1, 1, 1, 1, 8, 21, 21, 11, 11, 11, 2, 2, 2] 25 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 34, 24, 25, 33, 31] set([0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 122 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087031 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087031 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087031/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087031 Building REAL300004087032 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087032' /scratch/stefan/7774412/working/building/REAL300004087032 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087032 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087032/0 /scratch/stefan/7774412/working/building/REAL300004087032 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/45 `/scratch/stefan/7774412/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CNS(=O)(=O)C2=CC=C(C)C=C2)S1) `REAL300004087032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087032 none CC1=C(CC(=O)[O-])N=C(NC(=O)CNS(=O)(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 63, 63, 63, 35, 35, 35, 31, 35, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 63, 63, 35, 31, 31, 5, 1, 1, 2, 2, 2, 1, 1] 63 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087032 none CC1=C(CC(=O)[O-])N=C(NC(=O)CNS(=O)(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 14, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 2, 2, 2, 6, 6, 14, 35, 35, 35, 35, 35, 35, 35] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087032 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087032/1 /scratch/stefan/7774412/working/building/REAL300004087032 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/46 `/scratch/stefan/7774412/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNS(=O)(=O)C2=CC=C(C)C=C2)S1) `REAL300004087032.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087032/1/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: REAL300004087032 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNS(=O)(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 201, 201, 201, 147, 60, 26, 11, 26, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 201, 201, 11, 11, 5, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 588 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087032 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNS(=O)(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 36, 36, 74, 107, 147, 147, 147, 147, 147, 147, 147, 147, 147, 1, 2, 2, 2, 2, 2, 74, 74, 107, 147, 147, 147, 147, 147, 147, 147] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087032 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087032 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087032/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087032/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087032 Building REAL300004087033 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087033' /scratch/stefan/7774412/working/building/REAL300004087033 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087033 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087033/0 /scratch/stefan/7774412/working/building/REAL300004087033 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/47 `/scratch/stefan/7774412/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3N=CSC3=C2)S1) `REAL300004087033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087033 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3N=CSC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087033 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3N=CSC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087033 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087033 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087033/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087033 Building REAL300004087034 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087034' /scratch/stefan/7774412/working/building/REAL300004087034 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087034 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087034/0 /scratch/stefan/7774412/working/building/REAL300004087034 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/48 `/scratch/stefan/7774412/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1NC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087034 none COC1=CC=CC=C1NC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [51, 33, 33, 33, 16, 33, 33, 10, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 16, 16, 16, 16, 27, 48, 48, 16, 16, 16, 51, 51, 51, 33, 33, 33, 33, 10, 1, 1, 1, 16, 27, 27, 16, 16, 16] 137 rigid atoms, others: [36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087034 none COC1=CC=CC=C1NC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 33, 33, 33, 33, 33, 33, 98, 98, 102, 102, 102, 102, 136, 137, 137, 102, 102, 102, 3, 3, 3, 1, 1, 1, 1, 10, 33, 33, 33, 102, 136, 136, 102, 102, 102] 137 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087034 none COC1=CC=CC=C1NC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [115, 102, 102, 102, 86, 102, 102, 55, 16, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 115, 115, 115, 102, 102, 102, 102, 55, 16, 16, 16, 2, 2, 2, 2, 2, 2] 137 rigid atoms, others: [17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087034 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087034 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087034/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087034 Building REAL300004087035 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087035' /scratch/stefan/7774412/working/building/REAL300004087035 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087035 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087035/0 /scratch/stefan/7774412/working/building/REAL300004087035 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/49 `/scratch/stefan/7774412/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC2=CC=CC=C2F)S1) `REAL300004087035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087035 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC2=CC=CC=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 17, 23, 23, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 7, 15, 15, 15, 10, 10, 10, 10, 17, 17, 10, 1, 1, 1, 6, 15, 15, 14, 15] 43 rigid atoms, others: [33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087035 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC2=CC=CC=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 19, 33, 33, 25, 33, 33, 33, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 19, 33, 33, 32, 33] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087035 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC2=CC=CC=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 43, 43, 43, 33, 33, 33, 15, 33, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 43, 43, 33, 15, 15, 15, 7, 1, 1, 1, 1] 43 rigid atoms, others: [37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 135 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087035 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087035 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087035/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087035 Building REAL300004087036 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087036' /scratch/stefan/7774412/working/building/REAL300004087036 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087036 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087036/0 /scratch/stefan/7774412/working/building/REAL300004087036 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/50 `/scratch/stefan/7774412/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCS(=O)(=O)N2CCCC2)S1) `REAL300004087036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087036 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCS(=O)(=O)N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 36, 36, 36, 32, 32, 32, 29, 32, 15, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 32, 32, 32, 32, 36, 36, 32, 29, 29, 15, 15, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 15, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087036 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCS(=O)(=O)N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 14, 11, 11, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 7, 9, 29, 29, 29, 32, 32, 32, 32, 1, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 9, 9, 32, 32, 32, 32, 32, 32, 32, 32] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087036 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087036 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087036/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087036 Building REAL300004087037 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087037' /scratch/stefan/7774412/working/building/REAL300004087037 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087037 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087037/0 /scratch/stefan/7774412/working/building/REAL300004087037 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/51 `/scratch/stefan/7774412/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCN2C=CC=N2)S1) `REAL300004087037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087037 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCN2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 43, 43, 43, 29, 29, 29, 23, 29, 13, 9, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 43, 43, 29, 23, 23, 13, 13, 9, 9, 1, 1, 1] 43 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087037 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCN2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 8, 14, 29, 29, 29, 29, 1, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 14, 14, 29, 29, 29] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087037 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087037 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087037/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087037 Building REAL300004087038 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087038' /scratch/stefan/7774412/working/building/REAL300004087038 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087038 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087038/0 /scratch/stefan/7774412/working/building/REAL300004087038 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/52 `/scratch/stefan/7774412/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)SC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087038 none CC1=C(C)SC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087038 none CC1=C(C)SC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 14, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 13, 13, 13, 23, 23, 23, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 9, 23, 23, 13, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087038 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087038 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087038/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087038 Building REAL300004087039 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087039' /scratch/stefan/7774412/working/building/REAL300004087039 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087039 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087039/0 /scratch/stefan/7774412/working/building/REAL300004087039 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/53 `/scratch/stefan/7774412/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(CO)=C2)S1) `REAL300004087039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087039 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 38, 38, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 8, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 8, 8, 24, 1] 147 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087039 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(CO)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 38, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 38, 38, 114, 13] 147 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087039 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087039 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087039/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087039 Building REAL300004087040 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087040' /scratch/stefan/7774412/working/building/REAL300004087040 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087040 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087040/0 /scratch/stefan/7774412/working/building/REAL300004087040 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/54 `/scratch/stefan/7774412/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C2CCC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)CN12) `REAL300004087040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087040 none CC1=NN=C2CCC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 14, 15, 15, 15, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14] 28 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087040 none CC1=NN=C2CCC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)CN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 14, 14, 27, 28, 28, 14, 14, 14, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 27, 27, 15, 15, 15, 1, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 21, 22, 26, 27, 28, 29, 30, 37] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 31]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087040 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087040 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087040/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087040 Building REAL300004087041 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087041' /scratch/stefan/7774412/working/building/REAL300004087041 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087041 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087041/0 /scratch/stefan/7774412/working/building/REAL300004087041 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/55 `/scratch/stefan/7774412/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1) `REAL300004087041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087041 none CCN(CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 1, 7, 29, 59, 59, 59, 92, 92, 92, 163, 169, 169, 92, 92, 92, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 29, 29, 59, 163, 163, 92, 92, 92, 1, 1, 1, 1, 1] 201 rigid atoms, others: [2, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 756 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087041 none CCN(CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 59, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 59, 92, 92, 79, 92, 92, 106, 106, 106, 106, 106, 19, 19, 2, 2, 2, 2, 2, 2, 92, 92, 80, 92, 92] 201 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 551 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087041 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087041/1 /scratch/stefan/7774412/working/building/REAL300004087041 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/56 `/scratch/stefan/7774412/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1) `REAL300004087041.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087041/1/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: REAL300004087041 none CCN(CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 5, 10, 26, 26, 53, 76, 76, 76, 95, 99, 99, 76, 76, 76, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 10, 10, 95, 95, 76, 76, 76, 1, 1, 1, 1, 1] 107 rigid atoms, others: [2, 35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 301 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087041 none CCN(CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [90, 64, 50, 28, 11, 28, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 64, 76, 76, 76, 76, 76, 90, 90, 90, 90, 90, 50, 50, 2, 2, 2, 2, 2, 76, 76, 76, 76, 76] 107 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 388 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087041 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087041 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087041/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087041/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087041 Building REAL300004087042 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087042' /scratch/stefan/7774412/working/building/REAL300004087042 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087042 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087042/0 /scratch/stefan/7774412/working/building/REAL300004087042 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/57 `/scratch/stefan/7774412/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N=C(N(C)C)S3)S2)S1) `REAL300004087042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087042 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N=C(N(C)C)S3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 14, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 13, 13, 25, 25, 25, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 12, 13, 13, 13, 25, 25, 7, 1, 3, 3, 3, 3, 3, 3] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087042 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N=C(N(C)C)S3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'S.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 14, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 14, 14, 13, 12, 1, 2, 2, 2, 2, 2, 2, 13, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087042 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087042 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087042/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087042 Building REAL300004087043 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087043' /scratch/stefan/7774412/working/building/REAL300004087043 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087043 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087043/0 /scratch/stefan/7774412/working/building/REAL300004087043 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/58 `/scratch/stefan/7774412/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C(C)CCC2C)S1) `REAL300004087043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087043 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C(C)CCC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 33, 33, 33, 18, 15, 15, 6, 15, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 33, 33, 15, 6, 6, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2] 33 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 38, 39, 40]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087043 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C(C)CCC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087043 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087043 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087043/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087043 Building REAL300004087044 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087044' /scratch/stefan/7774412/working/building/REAL300004087044 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087044 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087044/0 /scratch/stefan/7774412/working/building/REAL300004087044 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/59 `/scratch/stefan/7774412/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C[NH+](C)C)=C2)S1) `REAL300004087044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087044 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C[NH+](C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1] 5 rigid atoms, others: [32, 41, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087044 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C[NH+](C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 5, 5, 5, 5, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087044 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087044 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087044/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087044 Building REAL300004087045 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087045' /scratch/stefan/7774412/working/building/REAL300004087045 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087045 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087045/0 /scratch/stefan/7774412/working/building/REAL300004087045 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/60 `/scratch/stefan/7774412/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](CC3=CC=CC=C3)C2)S1) `REAL300004087045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087045 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 3, 3, 3, 3, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 11 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 48, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087045 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 3, 3] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087045 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 11, 11, 11, 8, 8, 8, 5, 8, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5] 11 rigid atoms, others: [42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 50 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087045 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087045/1 /scratch/stefan/7774412/working/building/REAL300004087045 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/61 `/scratch/stefan/7774412/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](CC3=CC=CC=C3)C2)S1) `REAL300004087045.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087045 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 3, 3, 3, 3, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 11 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 48, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087045 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 3, 1, 2, 2, 2, 3, 3, 2, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 3, 3] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087045 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 11, 11, 11, 8, 8, 8, 5, 8, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 11, 11, 8, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 1, 1, 5, 5] 11 rigid atoms, others: [42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 45 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087045 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087045 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087045/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087045/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087045 Building REAL300004087046 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087046' /scratch/stefan/7774412/working/building/REAL300004087046 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087046 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087046/0 /scratch/stefan/7774412/working/building/REAL300004087046 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/62 `/scratch/stefan/7774412/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(F)=CC3=NC=CN=C23)S1) `REAL300004087046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087046 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(F)=CC3=NC=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 15, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 8, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087046 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(F)=CC3=NC=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 15, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087046 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087046 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087046/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087046 Building REAL300004087047 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087047' /scratch/stefan/7774412/working/building/REAL300004087047 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087047 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087047/0 /scratch/stefan/7774412/working/building/REAL300004087047 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/63 `/scratch/stefan/7774412/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCCC3)=N2)S1) `REAL300004087047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087047 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 13, 21, 36, 36, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 12, 13, 13, 13, 20, 21, 9, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 68 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087047 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 54, 54, 54, 54, 54, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54] 68 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087047 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 68, 68, 68, 54, 42, 42, 11, 42, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 54, 54, 54, 54, 68, 68, 42, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 204 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087047 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087047 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087047/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087047 Building REAL300004087048 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087048' /scratch/stefan/7774412/working/building/REAL300004087048 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087048 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087048/0 /scratch/stefan/7774412/working/building/REAL300004087048 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/64 `/scratch/stefan/7774412/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCCC3)N2)S1) `REAL300004087048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087048 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCCC3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087048 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCCC3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087048 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087048 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087048/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087048 Building REAL300004087049 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087049' /scratch/stefan/7774412/working/building/REAL300004087049 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087049 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087049/0 /scratch/stefan/7774412/working/building/REAL300004087049 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/65 `/scratch/stefan/7774412/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=NN1C) `REAL300004087049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087049 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 17, 17, 17, 17, 25, 25, 25, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17] 37 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 68 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087049 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 11, 11, 12, 17, 17, 17, 29, 35, 35, 17, 17, 17, 1, 1, 1, 1, 1, 3, 3, 3, 12, 29, 29, 17, 17, 17, 2, 2, 2, 2, 2, 2] 37 rigid atoms, others: [1, 2, 3, 4, 17, 18, 19, 20, 21] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 148 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087049 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087049 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087049/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087049 Building REAL300004087050 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087050' /scratch/stefan/7774412/working/building/REAL300004087050 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087050 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087050/0 /scratch/stefan/7774412/working/building/REAL300004087050 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/66 `/scratch/stefan/7774412/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2CCCC2)S1) `REAL300004087050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087050 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 13, 13, 13, 13, 25, 25, 10, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 25 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087050 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 7, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087050 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 10, 8, 2, 8, 2, 2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 10, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 108 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087050 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087050 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087050/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087050 Building REAL300004087051 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087051' /scratch/stefan/7774412/working/building/REAL300004087051 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087051 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087051/0 /scratch/stefan/7774412/working/building/REAL300004087051 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/67 `/scratch/stefan/7774412/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=CN=C2)S1) `REAL300004087051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087051 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 7, 7, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 3, 3, 3, 3, 5, 5, 3, 1, 2, 2, 2, 1, 1, 5, 5, 5] 9 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087051 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087051 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1] 9 rigid atoms, others: [37, 38, 39, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087051 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087051 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087051/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087051 Building REAL300004087052 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087052' /scratch/stefan/7774412/working/building/REAL300004087052 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087052 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087052/0 /scratch/stefan/7774412/working/building/REAL300004087052 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/68 `/scratch/stefan/7774412/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(NC3=CC=C(C)N=N3)=CC=C2)S1) `REAL300004087052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087052 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(NC3=CC=C(C)N=N3)=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 15, 34, 34, 9, 7, 7, 1, 7, 1, 1, 1, 1, 13, 46, 46, 46, 46, 46, 46, 1, 1, 1, 9, 9, 9, 9, 15, 15, 7, 1, 13, 46, 46, 46, 46, 46, 1, 1, 1] 170 rigid atoms, others: [33, 40, 41, 10, 12, 13, 14, 15, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087052 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(NC3=CC=C(C)N=N3)=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 9, 9, 9, 55, 103, 103, 103, 103, 103, 103, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 55, 103, 103, 103, 103, 103, 9, 9, 9] 170 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087052 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(NC3=CC=C(C)N=N3)=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 5, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 170, 170, 170, 103, 99, 99, 46, 99, 46, 46, 13, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 103, 103, 103, 103, 170, 170, 99, 46, 13, 1, 1, 2, 2, 2, 46, 46, 46] 170 rigid atoms, others: [35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 654 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087052 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087052 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087052/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087052 Building REAL300004087053 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087053' /scratch/stefan/7774412/working/building/REAL300004087053 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087053 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087053/0 /scratch/stefan/7774412/working/building/REAL300004087053 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/69 `/scratch/stefan/7774412/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=CN=CN32)S1) `REAL300004087053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087053 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=CN=CN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 7, 1, 1, 1] 17 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087053 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=CN=CN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 43 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087053 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087053 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087053/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087053 Building REAL300004087054 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087054' /scratch/stefan/7774412/working/building/REAL300004087054 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087054 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087054/0 /scratch/stefan/7774412/working/building/REAL300004087054 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/70 `/scratch/stefan/7774412/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCOCC2)S1) `REAL300004087054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087054 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 11, 11, 11, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087054 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 6, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087054 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087054/1 /scratch/stefan/7774412/working/building/REAL300004087054 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/71 `/scratch/stefan/7774412/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCOCC2)S1) `REAL300004087054.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087054/1/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: REAL300004087054 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 201, 201, 201, 173, 92, 52, 17, 52, 5, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 201, 201, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 496 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: REAL300004087054 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 42, 42, 106, 159, 173, 173, 173, 173, 173, 1, 2, 2, 2, 2, 2, 106, 106, 173, 173, 173, 173, 173, 173, 173, 173, 173] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 542 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087054 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087054 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087054/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087054/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087054 Building REAL300004087055 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087055' /scratch/stefan/7774412/working/building/REAL300004087055 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087055 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087055/0 /scratch/stefan/7774412/working/building/REAL300004087055 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/72 `/scratch/stefan/7774412/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(O)CC3)C=C2)S1) `REAL300004087055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087055 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(O)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 12, 19, 19, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7, 12, 12, 5, 1, 1, 7, 7, 7, 7, 7, 24, 7, 7, 7, 7, 1, 1] 84 rigid atoms, others: [32, 33, 45, 44, 10, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087055 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(O)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 5, 7, 20, 20, 20, 20, 20, 20, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 20, 20, 20, 20, 20, 59, 20, 20, 20, 20, 7, 7] 84 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087055 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(O)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 28, 28, 28, 20, 17, 16, 4, 16, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 20, 20, 28, 28, 17, 7, 7, 1, 1, 1, 1, 1, 6, 1, 1, 1, 1, 7, 7] 84 rigid atoms, others: [34, 35, 36, 37, 38, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 44, 45]) total number of confs: 116 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087055 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087055 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087055/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087055 Building REAL300004087056 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087056' /scratch/stefan/7774412/working/building/REAL300004087056 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087056 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087056/0 /scratch/stefan/7774412/working/building/REAL300004087056 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/73 `/scratch/stefan/7774412/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC(F)=C2N)S1) `REAL300004087056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087056 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC(F)=C2N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 16, 1, 1, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 9, 1, 1, 2, 2] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087056 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC(F)=C2N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 16, 1, 1, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 12, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087056 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087056 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087056/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087056 Building REAL300004087057 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087057' /scratch/stefan/7774412/working/building/REAL300004087057 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087057 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087057/0 /scratch/stefan/7774412/working/building/REAL300004087057 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/74 `/scratch/stefan/7774412/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)OCCC2=CC=CC=C2)S1) `REAL300004087057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087057 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)OCCC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 201, 201, 201, 127, 108, 106, 42, 106, 15, 42, 5, 3, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 201, 201, 108, 42, 42, 42, 42, 5, 5, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 822 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087057 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)OCCC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 15, 41, 82, 125, 127, 127, 126, 127, 127, 1, 2, 2, 2, 2, 2, 2, 17, 18, 18, 18, 82, 82, 125, 125, 127, 127, 127, 127, 127] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087057 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087057/1 /scratch/stefan/7774412/working/building/REAL300004087057 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/75 `/scratch/stefan/7774412/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)OCCC2=CC=CC=C2)S1) `REAL300004087057.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087057/1/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: REAL300004087057 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)OCCC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 201, 201, 201, 169, 102, 61, 28, 61, 14, 28, 5, 2, 1, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 201, 201, 28, 28, 28, 28, 5, 5, 2, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 567 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087057 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)OCCC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 29, 29, 53, 53, 72, 133, 168, 169, 169, 169, 169, 169, 1, 2, 2, 2, 2, 2, 53, 53, 53, 53, 133, 133, 168, 168, 169, 169, 169, 169, 169] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087057 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087057 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087057/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087057/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087057 Building REAL300004087058 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087058' /scratch/stefan/7774412/working/building/REAL300004087058 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087058 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087058/0 /scratch/stefan/7774412/working/building/REAL300004087058 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/76 `/scratch/stefan/7774412/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN=C2C2CC2)S1) `REAL300004087058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087058 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 25, 27, 27, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 25, 25, 10, 1, 1, 5, 5, 5, 5, 5] 48 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087058 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 5, 14, 14, 14, 27, 27, 1, 2, 2, 2, 2, 2, 2, 14, 13, 27, 27, 27, 27, 27] 48 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087058 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 48, 48, 48, 27, 19, 15, 5, 15, 5, 5, 5, 5, 5, 1, 1, 1, 1, 27, 27, 27, 27, 48, 48, 19, 5, 5, 1, 1, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 190 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087058 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087058 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087058/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087058 Building REAL300004087059 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087059' /scratch/stefan/7774412/working/building/REAL300004087059 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087059 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087059/0 /scratch/stefan/7774412/working/building/REAL300004087059 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/77 `/scratch/stefan/7774412/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2C2CC2)S1) `REAL300004087059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087059 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 25, 29, 29, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 25, 25, 10, 1, 2, 2, 2, 5, 5, 5, 5, 5] 47 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087059 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 13, 13, 14, 14, 14, 27, 27, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 27, 27, 27, 27, 27] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087059 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 47, 47, 47, 27, 19, 15, 5, 15, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 27, 27, 27, 27, 47, 47, 19, 5, 5, 5, 5, 1, 1, 1, 1, 1] 47 rigid atoms, others: [33, 34, 35, 36, 37, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 184 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087059 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087059 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087059/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087059 Building REAL300004087060 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087060' /scratch/stefan/7774412/working/building/REAL300004087060 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087060 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087060/0 /scratch/stefan/7774412/working/building/REAL300004087060 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/78 `/scratch/stefan/7774412/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CN=CN2C)S1) `REAL300004087060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087060 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CN=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 15, 15, 15, 11, 11, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 11, 9, 9, 5, 5, 1, 1, 2, 2, 2] 15 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087060 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CN=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 4, 6, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 11, 11, 11, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087060 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087060 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087060/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087060 Building REAL300004087061 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087061' /scratch/stefan/7774412/working/building/REAL300004087061 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087061 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087061/0 /scratch/stefan/7774412/working/building/REAL300004087061 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/79 `/scratch/stefan/7774412/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC(C)C)CCCC2)S1) `REAL300004087061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087061 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC(C)C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 5, 5, 1, 5, 1, 1, 3, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 12, 13, 44, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087061 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC(C)C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087061 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087061/1 /scratch/stefan/7774412/working/building/REAL300004087061 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/80 `/scratch/stefan/7774412/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC(C)C)CCCC2)S1) `REAL300004087061.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087061/1/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: REAL300004087061 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC(C)C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [112, 112, 112, 112, 165, 165, 165, 112, 19, 5, 1, 5, 1, 1, 3, 3, 3, 1, 1, 1, 1, 112, 112, 112, 112, 165, 165, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 165 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 17, 18, 19, 20, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 465 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087061 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC(C)C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 12, 56, 56, 112, 112, 112, 112, 112, 112, 112, 112, 1, 2, 2, 2, 2, 2, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112] 165 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 335 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087061 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087061 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087061/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087061/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087061 Building REAL300004087062 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087062' /scratch/stefan/7774412/working/building/REAL300004087062 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087062 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087062/0 /scratch/stefan/7774412/working/building/REAL300004087062 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/81 `/scratch/stefan/7774412/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2(C)CCOCC2)S1) `REAL300004087062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087062 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2(C)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 56, 57, 57, 36, 36, 32, 8, 32, 8, 1, 1, 1, 1, 1, 1, 1, 1, 36, 37, 37, 37, 56, 56, 36, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087062 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2(C)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 12, 12, 36, 36, 36, 36, 36, 36, 1, 2, 2, 2, 2, 2, 2, 12, 12, 37, 37, 37, 36, 36, 36, 36, 36, 36, 36, 36] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087062 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087062 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087062/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087062 Building REAL300004087063 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087063' /scratch/stefan/7774412/working/building/REAL300004087063 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087063 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087063/0 /scratch/stefan/7774412/working/building/REAL300004087063 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/82 `/scratch/stefan/7774412/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(S(C)(=O)=O)CC2)S1) `REAL300004087063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087063 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(S(C)(=O)=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 11, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 40, 50, 50, 23, 14, 13, 1, 13, 1, 1, 8, 8, 8, 1, 1, 23, 23, 23, 23, 40, 40, 14, 8, 8, 8, 1, 1, 1, 1] 58 rigid atoms, others: [32, 10, 12, 13, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 215 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087063 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(S(C)(=O)=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 11, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 23, 41, 41, 41, 23, 23, 1, 2, 2, 2, 2, 2, 3, 41, 41, 41, 23, 23, 23, 23] 58 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087063 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087063/1 /scratch/stefan/7774412/working/building/REAL300004087063 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/83 `/scratch/stefan/7774412/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(S(C)(=O)=O)CC2)S1) `REAL300004087063.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087063/1/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: REAL300004087063 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(S(C)(=O)=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 11, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 1, 3, 1, 1, 3, 3, 3, 1, 1, 3, 3, 3, 3, 4, 4, 3, 3, 3, 1, 1, 1, 1] 4 rigid atoms, others: [10, 12, 13, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087063 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(S(C)(=O)=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 5, 11, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3] 4 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087063 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087063 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087063/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087063/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087063 Building REAL300004087064 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087064' /scratch/stefan/7774412/working/building/REAL300004087064 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087064 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087064/0 /scratch/stefan/7774412/working/building/REAL300004087064 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/84 `/scratch/stefan/7774412/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C(C)(C)C)S1) `REAL300004087064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087064 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 15, 15, 6, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 17 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087064 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 8, 8, 8, 8, 8, 8, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087064 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087064 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087064/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087064 Building REAL300004087065 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087065' /scratch/stefan/7774412/working/building/REAL300004087065 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087065 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087065/0 /scratch/stefan/7774412/working/building/REAL300004087065 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/85 `/scratch/stefan/7774412/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CN=C2)C(C)C)S1) `REAL300004087065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087065 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CN=C2)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 35, 35, 35, 22, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 22, 22, 22, 22, 35, 35, 15, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 35 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087065 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CN=C2)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 12, 22, 22, 22, 22, 22, 12, 12, 12, 1, 2, 2, 2, 2, 2, 3, 12, 22, 22, 22, 22, 12, 12, 12, 12, 12, 12, 12] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087065 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087065/1 /scratch/stefan/7774412/working/building/REAL300004087065 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/86 `/scratch/stefan/7774412/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CN=C2)C(C)C)S1) `REAL300004087065.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087065/1/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: REAL300004087065 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CN=C2)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [130, 130, 130, 130, 179, 179, 179, 130, 51, 13, 5, 13, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 130, 130, 130, 130, 179, 179, 5, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11] 179 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 514 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087065 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CN=C2)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 7, 7, 1, 1, 1, 12, 45, 45, 73, 130, 130, 130, 130, 130, 73, 77, 77, 1, 2, 2, 2, 2, 2, 73, 130, 130, 130, 130, 77, 77, 77, 77, 77, 77, 77] 179 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087065 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087065 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087065/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087065/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087065 Building REAL300004087066 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087066' /scratch/stefan/7774412/working/building/REAL300004087066 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087066 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087066/0 /scratch/stefan/7774412/working/building/REAL300004087066 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/87 `/scratch/stefan/7774412/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC(C)=CC(F)=C3)N=N2)S1) `REAL300004087066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087066 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC(C)=CC(F)=C3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 1, 15, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 29, 29, 29, 16, 13, 11, 1, 11, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 1, 1, 16, 16, 16, 16, 29, 29, 13, 1, 7, 7, 7, 7, 6, 7] 57 rigid atoms, others: [32, 10, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087066 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC(C)=CC(F)=C3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 1, 15, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 35, 35, 35, 35, 35, 35, 35, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 35, 35, 35, 35, 35, 35] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087066 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC(C)=CC(F)=C3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 1, 1, 15, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 57, 57, 57, 35, 29, 25, 7, 25, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 35, 35, 35, 35, 57, 57, 29, 7, 1, 2, 2, 2, 1, 1] 57 rigid atoms, others: [33, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 214 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087066 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087066 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087066/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087066 Building REAL300004087067 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087067' /scratch/stefan/7774412/working/building/REAL300004087067 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087067 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087067/0 /scratch/stefan/7774412/working/building/REAL300004087067 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/88 `/scratch/stefan/7774412/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C1=NC(C)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1) `REAL300004087067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087067 none COC(C)(C)C1=NC(C)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [111, 97, 20, 97, 97, 20, 20, 20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 111, 111, 111, 97, 97, 97, 97, 97, 97, 20, 20, 20, 2, 2, 2, 2, 2, 2] 157 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087067 none COC(C)(C)C1=NC(C)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [38, 13, 1, 13, 13, 1, 1, 1, 1, 1, 1, 9, 9, 11, 20, 20, 20, 37, 58, 58, 20, 20, 20, 1, 38, 38, 38, 13, 13, 13, 13, 13, 13, 2, 2, 2, 11, 37, 37, 20, 20, 20] 157 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 23] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087067 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087067 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087067/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087067 Building REAL300004087068 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087068' /scratch/stefan/7774412/working/building/REAL300004087068 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087068 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087068/0 /scratch/stefan/7774412/working/building/REAL300004087068 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/89 `/scratch/stefan/7774412/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1) `REAL300004087068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087068 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 15, 8, 8, 1, 2, 2, 1, 2, 2] 21 rigid atoms, others: [33, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 37, 38]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087068 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 6, 6, 15, 15, 15, 15, 15, 15] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087068 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 15, 8, 8, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 85 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087068 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087068/1 /scratch/stefan/7774412/working/building/REAL300004087068 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/90 `/scratch/stefan/7774412/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1) `REAL300004087068.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087068 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 201, 201, 201, 159, 87, 33, 8, 33, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 159, 159, 159, 159, 201, 201, 8, 8, 1, 4, 4, 2, 4, 4] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087068 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 32, 32, 106, 159, 159, 159, 159, 173, 173, 161, 173, 173, 159, 1, 2, 2, 2, 2, 2, 106, 106, 159, 173, 173, 173, 173, 173] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087068 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 201, 201, 201, 173, 118, 62, 18, 62, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 173, 173, 173, 173, 201, 201, 18, 18, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 523 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087068 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087068 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087068/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087068/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087068 Building REAL300004087069 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087069' /scratch/stefan/7774412/working/building/REAL300004087069 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087069 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087069/0 /scratch/stefan/7774412/working/building/REAL300004087069 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/91 `/scratch/stefan/7774412/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=NC=N2)S1) `REAL300004087069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087069 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [19, 20, 20, 20, 34, 46, 46, 20, 15, 11, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 20, 20, 20, 20, 34, 34, 15, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1] 77 rigid atoms, others: [40, 10, 12, 13, 14, 15, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 196 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: REAL300004087069 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 20, 20, 53, 53, 53, 53, 53, 19, 20, 20, 1, 2, 2, 2, 2, 2, 2, 20, 53, 53, 53, 53, 53, 53, 53, 53, 20] 77 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087069 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [52, 53, 53, 53, 77, 77, 77, 53, 44, 40, 8, 40, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 53, 53, 53, 53, 77, 77, 44, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8] 77 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40]) total number of confs: 270 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087069 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087069 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087069/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087069 Building REAL300004087070 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087070' /scratch/stefan/7774412/working/building/REAL300004087070 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087070 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087070/0 /scratch/stefan/7774412/working/building/REAL300004087070 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/92 `/scratch/stefan/7774412/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=N[N-]N=N2)S1) `REAL300004087070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087070 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=N[N-]N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 143, 143, 143, 116, 83, 81, 17, 81, 8, 4, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 143, 143, 83, 17, 17, 8, 8, 4, 4] 143 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087070 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=N[N-]N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 20, 36, 77, 105, 105, 105, 105, 1, 2, 2, 2, 2, 2, 3, 20, 20, 44, 44, 73, 73] 142 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087070 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087070/1 /scratch/stefan/7774412/working/building/REAL300004087070 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/93 `/scratch/stefan/7774412/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=NN=N[N-]2)S1) `REAL300004087070.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087070/1/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: REAL300004087070 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=NN=N[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 148, 148, 148, 117, 84, 83, 17, 83, 8, 4, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 148, 148, 84, 17, 17, 8, 8, 4, 4] 148 rigid atoms, others: [14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087070 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=NN=N[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 20, 36, 76, 108, 108, 108, 108, 1, 2, 2, 2, 2, 2, 3, 20, 20, 44, 44, 72, 72] 148 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087070 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087070 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087070/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087070/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087070 Building REAL300004087071 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087071' /scratch/stefan/7774412/working/building/REAL300004087071 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087071 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087071/0 /scratch/stefan/7774412/working/building/REAL300004087071 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/94 `/scratch/stefan/7774412/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087071 none COCC(C)C(C)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 154 conformations in input total number of sets (complete confs): 154 using faster count positions algorithm for large data unique positions, atoms: [115, 103, 51, 20, 50, 3, 20, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 115, 115, 115, 104, 103, 54, 54, 54, 54, 20, 21, 21, 21, 2, 2, 2, 2, 2, 2] 154 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 536 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087071 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087071 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087071/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087071 Building REAL300004087072 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087072' /scratch/stefan/7774412/working/building/REAL300004087072 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087072 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087072/0 /scratch/stefan/7774412/working/building/REAL300004087072 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/95 `/scratch/stefan/7774412/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCC(C)CC1) `REAL300004087072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087072 none CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 1, 8, 22, 22, 23, 32, 32, 32, 56, 61, 61, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 8, 23, 56, 56, 32, 32, 32, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 61 rigid atoms, others: [2, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 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, 41, 42, 43]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087072 none CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCC(C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [17, 16, 4, 2, 4, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 16, 30, 32, 32, 32, 32, 31, 21, 21, 21, 21, 21, 16, 2, 3, 3, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 61 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087072 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087072 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087072/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087072 Building REAL300004087073 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087073' /scratch/stefan/7774412/working/building/REAL300004087073 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087073 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087073/0 /scratch/stefan/7774412/working/building/REAL300004087073 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/96 `/scratch/stefan/7774412/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1C1=CC=CC=C1) `REAL300004087073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087073 none COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [119, 85, 27, 27, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 27, 27, 27, 27, 62, 62, 44, 62, 62, 119, 119, 119, 85, 85, 2, 2, 2, 2, 2, 2, 27, 62, 62, 45, 62, 62] 183 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 455 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087073 none COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [28, 7, 1, 1, 1, 1, 12, 12, 16, 27, 27, 27, 50, 81, 81, 27, 27, 27, 1, 1, 1, 1, 5, 5, 3, 5, 5, 28, 28, 28, 7, 7, 16, 50, 50, 28, 28, 28, 1, 5, 5, 3, 5, 5] 183 rigid atoms, others: [2, 3, 4, 5, 38, 18, 19, 20, 21] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43]) total number of confs: 383 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087073 none COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [47, 19, 5, 5, 5, 5, 37, 37, 41, 62, 62, 62, 112, 134, 134, 62, 62, 62, 5, 5, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 19, 19, 41, 112, 112, 62, 62, 62, 5, 1, 1, 1, 1, 1] 183 rigid atoms, others: [39, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 620 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087073 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087073 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087073/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087073 Building REAL300004087074 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087074' /scratch/stefan/7774412/working/building/REAL300004087074 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087074 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087074/0 /scratch/stefan/7774412/working/building/REAL300004087074 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/97 `/scratch/stefan/7774412/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C(F)(F)F)S1) `REAL300004087074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087074 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 21, 21, 9, 1, 1] 21 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087074 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087074 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087074 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087074/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087074 Building REAL300004087075 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087075' /scratch/stefan/7774412/working/building/REAL300004087075 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087075 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087075/0 /scratch/stefan/7774412/working/building/REAL300004087075 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/98 `/scratch/stefan/7774412/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3CC3)=C2)S1) `REAL300004087075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087075 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 23, 32, 32, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 13, 13, 13, 13, 23, 23, 9, 1, 1, 6, 6, 6, 6, 6, 1] 64 rigid atoms, others: [36, 10, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) 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: REAL300004087075 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 38, 38, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 38, 38, 38, 38, 38, 13] 64 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087075 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 64, 64, 64, 38, 30, 26, 6, 26, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 38, 38, 38, 38, 64, 64, 30, 6, 6, 1, 1, 1, 1, 1, 6] 64 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36]) total number of confs: 243 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087075 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087075 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087075/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087075 Building REAL300004087076 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087076' /scratch/stefan/7774412/working/building/REAL300004087076 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087076 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087076/0 /scratch/stefan/7774412/working/building/REAL300004087076 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/99 `/scratch/stefan/7774412/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=N1) `REAL300004087076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087076 none CC(=O)C1=CN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2] 13 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087076 none CC(=O)C1=CN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 1, 2, 2, 2, 1, 7, 7, 7, 13, 13, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087076 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087076/1 /scratch/stefan/7774412/working/building/REAL300004087076 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/100 `/scratch/stefan/7774412/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=N1) `REAL300004087076.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087076/1/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: REAL300004087076 none CC(=O)C1=CN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 9, 9, 9, 9, 6, 9, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 9, 9, 11, 11, 11, 9, 9, 9, 3, 3, 2, 2, 2] 11 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087076 none CC(=O)C1=CN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 3, 3, 3, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 5, 4, 4, 1, 3, 3, 9, 9, 9, 9, 9] 11 rigid atoms, others: [1, 3, 4, 5, 6, 20, 21, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087076 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087076 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087076/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087076/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087076 Building REAL300004087077 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087077' /scratch/stefan/7774412/working/building/REAL300004087077 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087077 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087077/0 /scratch/stefan/7774412/working/building/REAL300004087077 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/101 `/scratch/stefan/7774412/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(C(F)(F)F)CC2)S1) `REAL300004087077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087077 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(C(F)(F)F)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 3, 3, 2, 2, 2, 1, 1, 1, 1] 3 rigid atoms, others: [32, 12, 13, 14, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087077 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(C(F)(F)F)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 15, 15, 15, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087077 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087077 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087077/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087077 Building REAL300004087078 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087078' /scratch/stefan/7774412/working/building/REAL300004087078 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087078 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087078/0 /scratch/stefan/7774412/working/building/REAL300004087078 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/102 `/scratch/stefan/7774412/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC3=CC=NN32)S1) `REAL300004087078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087078 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 9, 13, 13, 13, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 12, 13, 7, 1, 1, 1, 1] 13 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087078 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 8, 8, 4, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087078 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087078 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087078/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087078 Building REAL300004087079 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087079' /scratch/stefan/7774412/working/building/REAL300004087079 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087079 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087079/0 /scratch/stefan/7774412/working/building/REAL300004087079 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/103 `/scratch/stefan/7774412/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CC3CCC2O3)S1) `REAL300004087079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087079 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CC3CCC2O3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 19, 19, 19, 13, 13, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 19, 19, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087079 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CC3CCC2O3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087079 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087079 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087079/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087079 Building REAL300004087080 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087080' /scratch/stefan/7774412/working/building/REAL300004087080 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087080 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087080/0 /scratch/stefan/7774412/working/building/REAL300004087080 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/104 `/scratch/stefan/7774412/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC3=C(C)C=CN=C23)S1) `REAL300004087080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087080 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC3=C(C)C=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 8, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1] 19 rigid atoms, others: [35, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087080 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC3=C(C)C=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 5, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087080 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087080 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087080/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087080 Building REAL300004087081 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087081' /scratch/stefan/7774412/working/building/REAL300004087081 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087081 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087081/0 /scratch/stefan/7774412/working/building/REAL300004087081 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/105 `/scratch/stefan/7774412/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=CN=C3)N=C2)S1) `REAL300004087081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087081 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=CN=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 21, 23, 23, 13, 9, 7, 1, 7, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 13, 13, 13, 13, 21, 21, 9, 1, 3, 3, 2, 3, 1] 39 rigid atoms, others: [35, 10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087081 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=CN=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 23, 23, 23, 23, 23, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 23, 23, 23, 23, 13] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087081 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=CN=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 39, 39, 39, 23, 15, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 23, 23, 23, 23, 39, 39, 15, 3, 1, 1, 1, 1, 3] 39 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 148 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087081 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087081 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087081/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087081 Building REAL300004087082 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087082' /scratch/stefan/7774412/working/building/REAL300004087082 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087082 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087082/0 /scratch/stefan/7774412/working/building/REAL300004087082 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/106 `/scratch/stefan/7774412/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C(C)O)N=N2)S1) `REAL300004087082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087082 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C(C)O)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 18, 28, 28, 12, 12, 12, 8, 12, 1, 1, 1, 1, 1, 8, 8, 1, 1, 12, 12, 12, 12, 18, 18, 12, 8, 8, 1, 8, 8, 8, 8, 24] 132 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087082 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C(C)O)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 12, 12, 12, 28, 28, 12, 12, 1, 2, 2, 2, 2, 2, 2, 6, 6, 12, 28, 28, 28, 28, 84] 132 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087082 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087082/1 /scratch/stefan/7774412/working/building/REAL300004087082 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/107 `/scratch/stefan/7774412/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C(C)O)N=N2)S1) `REAL300004087082.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087082/1/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: REAL300004087082 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C(C)O)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 76, 91, 91, 71, 39, 24, 8, 24, 1, 1, 1, 1, 1, 12, 12, 1, 1, 71, 71, 71, 71, 76, 76, 8, 8, 1, 12, 12, 12, 12, 36] 378 rigid atoms, others: [12, 13, 14, 15, 16, 19, 20, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) 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: REAL300004087082 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C(C)O)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 40, 40, 58, 71, 71, 71, 123, 123, 71, 71, 1, 2, 2, 2, 2, 2, 58, 58, 71, 123, 123, 123, 123, 369] 378 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 878 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087082 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087082 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087082/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087082/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087082 Building REAL300004087083 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087083' /scratch/stefan/7774412/working/building/REAL300004087083 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087083 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087083/0 /scratch/stefan/7774412/working/building/REAL300004087083 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/108 `/scratch/stefan/7774412/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C3=CC=CC=C3)=CS2)S1) `REAL300004087083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087083 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 23, 23, 38, 46, 46, 22, 16, 12, 1, 12, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 22, 23, 23, 23, 38, 38, 16, 7, 7, 6, 7, 7, 1] 62 rigid atoms, others: [35, 10, 12, 13, 14, 15, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087083 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 22, 22, 22, 49, 49, 40, 49, 49, 22, 22, 1, 2, 2, 2, 2, 2, 2, 49, 49, 48, 49, 49, 22] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087083 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 62, 62, 62, 49, 44, 40, 7, 40, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 49, 49, 49, 49, 62, 62, 44, 1, 1, 1, 1, 1, 7] 62 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 190 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087083 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087083 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087083/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087083 Building REAL300004087084 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087084' /scratch/stefan/7774412/working/building/REAL300004087084 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087084 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087084/0 /scratch/stefan/7774412/working/building/REAL300004087084 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/109 `/scratch/stefan/7774412/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C(C)C)=C(C)S2)S1) `REAL300004087084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087084 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C(C)C)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 5, 5, 5, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 53, 53, 53, 34, 34, 34, 8, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 53, 53, 34, 8, 8, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 53 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087084 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C(C)C)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 5, 5, 5, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 14, 34, 34, 34, 34, 34, 34, 34, 34, 1, 2, 2, 2, 2, 2, 2, 14, 14, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087084 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087084/1 /scratch/stefan/7774412/working/building/REAL300004087084 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/110 `/scratch/stefan/7774412/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C(C)C)=C(C)S2)S1) `REAL300004087084.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087084/1/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: REAL300004087084 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C(C)C)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 5, 5, 5, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 83, 35, 8, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 201, 201, 8, 8, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) 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: REAL300004087084 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C(C)C)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 5, 5, 5, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 35, 35, 100, 167, 167, 167, 167, 167, 167, 167, 167, 1, 2, 2, 2, 3, 3, 100, 100, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 489 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087084 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087084 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087084/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087084/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087084 Building REAL300004087085 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087085' /scratch/stefan/7774412/working/building/REAL300004087085 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087085 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087085/0 /scratch/stefan/7774412/working/building/REAL300004087085 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/111 `/scratch/stefan/7774412/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=NC=CS2)S1) `REAL300004087085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087085 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 39, 39, 39, 23, 23, 22, 20, 22, 10, 4, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 39, 39, 23, 20, 20, 10, 10, 4, 4, 1, 1] 39 rigid atoms, others: [33, 34, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 196 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087085 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 6, 10, 23, 23, 23, 23, 1, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 10, 10, 23, 23] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087085 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087085 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087085/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087085 Building REAL300004087086 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087086' /scratch/stefan/7774412/working/building/REAL300004087086 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087086 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087086/0 /scratch/stefan/7774412/working/building/REAL300004087086 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/112 `/scratch/stefan/7774412/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(N3CCOCC3)=N2)S1) `REAL300004087086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087086 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(N3CCOCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 35, 43, 43, 20, 20, 20, 7, 20, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 20, 20, 20, 20, 35, 35, 20, 7, 7, 1, 8, 8, 8, 8, 8, 8, 8, 8] 73 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087086 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(N3CCOCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 11, 20, 20, 20, 20, 51, 51, 51, 51, 51, 20, 1, 2, 2, 2, 2, 2, 2, 11, 11, 20, 51, 51, 51, 51, 51, 51, 51, 51] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087086 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(N3CCOCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 73, 73, 73, 51, 51, 51, 22, 51, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 51, 51, 51, 51, 73, 73, 51, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087086 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087086/1 /scratch/stefan/7774412/working/building/REAL300004087086 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/113 `/scratch/stefan/7774412/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(N3CCOCC3)=N2)S1) `REAL300004087086.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087086 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(N3CCOCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 119, 126, 126, 97, 45, 20, 5, 20, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 97, 97, 97, 97, 119, 119, 5, 5, 1, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087086 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(N3CCOCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 29, 29, 74, 97, 97, 97, 97, 181, 181, 181, 181, 181, 97, 1, 2, 2, 2, 3, 3, 74, 74, 97, 181, 181, 181, 181, 181, 181, 181, 181] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087086 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(N3CCOCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 12, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 181, 181, 201, 201, 201, 181, 112, 68, 22, 68, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 181, 181, 181, 181, 201, 201, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 499 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087086 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087086 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087086/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087086/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087086 Building REAL300004087087 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087087' /scratch/stefan/7774412/working/building/REAL300004087087 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087087 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087087/0 /scratch/stefan/7774412/working/building/REAL300004087087 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/114 `/scratch/stefan/7774412/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCC(O)CCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087087 none CCCCCCCCC(O)CCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [137, 120, 85, 60, 37, 24, 23, 14, 9, 14, 9, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 146, 150, 150, 150, 148, 136, 137, 93, 94, 62, 62, 37, 37, 24, 24, 23, 23, 14, 42, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 603 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 953 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087087 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087087 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087087/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087087 Building REAL300004087088 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087088' /scratch/stefan/7774412/working/building/REAL300004087088 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087088 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087088/0 /scratch/stefan/7774412/working/building/REAL300004087088 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/115 `/scratch/stefan/7774412/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1) `REAL300004087088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087088 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 44, 54, 54, 28, 28, 27, 7, 28, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 28, 28, 28, 28, 44, 44, 28, 7, 7, 5, 5, 1, 5, 5, 1] 67 rigid atoms, others: [38, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087088 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 14, 28, 28, 28, 49, 49, 34, 49, 49, 28, 28, 1, 2, 2, 2, 2, 2, 2, 14, 14, 49, 49, 43, 49, 49, 28] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087088 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 47, 49, 67, 67, 67, 49, 49, 49, 21, 49, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 49, 49, 49, 49, 67, 67, 49, 21, 21, 1, 1, 1, 1, 1, 5] 67 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 256 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087088 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087088/1 /scratch/stefan/7774412/working/building/REAL300004087088 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/116 `/scratch/stefan/7774412/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1) `REAL300004087088.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087088 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 155, 161, 161, 115, 56, 26, 6, 27, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 1, 115, 115, 115, 115, 155, 155, 6, 6, 7, 7, 1, 7, 7, 1] 201 rigid atoms, others: [37, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087088 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 11, 26, 26, 66, 115, 115, 115, 175, 175, 141, 175, 175, 115, 115, 1, 2, 2, 2, 2, 2, 66, 66, 175, 175, 161, 175, 175, 115] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 562 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087088 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CC=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 201, 201, 201, 175, 117, 72, 23, 72, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 175, 175, 175, 175, 201, 201, 23, 23, 1, 1, 1, 1, 1, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 532 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087088 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087088 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087088/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087088/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087088 Building REAL300004087089 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087089' /scratch/stefan/7774412/working/building/REAL300004087089 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087089 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087089/0 /scratch/stefan/7774412/working/building/REAL300004087089 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/117 `/scratch/stefan/7774412/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3=CC=CC=C3C2)S1) `REAL300004087089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087089 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3=CC=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 99 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087089 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3=CC=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087089 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087089 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087089/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087089 Building REAL300004087090 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087090' /scratch/stefan/7774412/working/building/REAL300004087090 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087090 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087090/0 /scratch/stefan/7774412/working/building/REAL300004087090 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/118 `/scratch/stefan/7774412/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CN=C3)SC=N2)S1) `REAL300004087090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087090 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CN=C3)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 9, 9, 15, 33, 33, 9, 5, 6, 1, 5, 1, 1, 1, 6, 21, 21, 21, 21, 21, 1, 1, 1, 8, 9, 9, 9, 15, 15, 6, 6, 21, 21, 21, 21, 1] 72 rigid atoms, others: [36, 10, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087090 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CN=C3)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 9, 20, 39, 39, 39, 39, 39, 8, 9, 9, 1, 2, 2, 2, 2, 2, 2, 20, 39, 39, 39, 39, 9] 72 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087090 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CN=C3)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 72, 72, 72, 39, 29, 29, 21, 29, 21, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 39, 39, 39, 39, 72, 72, 29, 11, 1, 1, 1, 1, 21] 72 rigid atoms, others: [32, 33, 34, 35, 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, 36]) total number of confs: 289 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087090 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087090 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087090/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087090 Building REAL300004087091 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087091' /scratch/stefan/7774412/working/building/REAL300004087091 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087091 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087091/0 /scratch/stefan/7774412/working/building/REAL300004087091 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/119 `/scratch/stefan/7774412/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1) `REAL300004087091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087091 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 21, 25, 25, 14, 14, 14, 6, 14, 1, 1, 1, 1, 1, 1, 5, 5, 2, 5, 5, 1, 1, 14, 14, 14, 14, 21, 21, 14, 6, 6, 5, 5, 2, 5, 5, 2, 2, 2] 26 rigid atoms, others: [12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 121 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087091 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 14, 14, 14, 14, 22, 22, 20, 22, 22, 14, 14, 1, 2, 2, 2, 2, 2, 2, 6, 6, 22, 22, 20, 22, 22, 14, 14, 14] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087091 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 26, 26, 26, 22, 22, 22, 13, 22, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 22, 22, 22, 26, 26, 22, 13, 13, 1, 1, 1, 1, 1, 5, 5, 5] 26 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41]) total number of confs: 94 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087091 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087091/1 /scratch/stefan/7774412/working/building/REAL300004087091 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/120 `/scratch/stefan/7774412/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1) `REAL300004087091.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087091 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 193, 201, 201, 152, 63, 23, 7, 23, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 1, 1, 152, 152, 152, 152, 193, 193, 7, 7, 4, 4, 3, 4, 4, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 544 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087091 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 59, 59, 122, 152, 152, 152, 152, 183, 183, 183, 183, 183, 152, 152, 1, 2, 2, 2, 2, 2, 122, 122, 183, 183, 183, 183, 183, 152, 152, 152] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087091 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN=C(C3=CC=CC=C3)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 183, 183, 183, 201, 201, 201, 183, 99, 41, 16, 41, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 183, 183, 183, 183, 201, 201, 16, 16, 1, 1, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 438 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087091 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087091 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087091/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087091/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087091 Building REAL300004087092 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087092' /scratch/stefan/7774412/working/building/REAL300004087092 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087092 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087092/0 /scratch/stefan/7774412/working/building/REAL300004087092 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/121 `/scratch/stefan/7774412/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC(O)C2=CC=CC=C2)S1) `REAL300004087092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087092 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC(O)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 33, 33, 33, 20, 20, 20, 16, 20, 13, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 33, 33, 20, 16, 16, 13, 13, 10, 10, 4, 12, 1, 1, 1, 1, 1] 99 rigid atoms, others: [38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 172 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087092 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC(O)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 8, 10, 19, 19, 20, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 5, 5, 8, 8, 10, 10, 19, 57, 20, 20, 20, 20, 20] 99 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 158 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087092 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087092 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087092/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087092 Building REAL300004087093 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087093' /scratch/stefan/7774412/working/building/REAL300004087093 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087093 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087093/0 /scratch/stefan/7774412/working/building/REAL300004087093 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/122 `/scratch/stefan/7774412/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=NC=C2)S1) `REAL300004087093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087093 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [38, 38, 38, 38, 63, 63, 63, 38, 34, 31, 7, 31, 1, 7, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 63, 63, 34, 7, 7, 7, 7, 1, 1, 1, 1] 63 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087093 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 38, 38, 36, 38, 38, 1, 2, 2, 2, 3, 3, 2, 22, 23, 23, 23, 38, 38, 38, 38] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087093 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087093/1 /scratch/stefan/7774412/working/building/REAL300004087093 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/123 `/scratch/stefan/7774412/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=NC=C2)S1) `REAL300004087093.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087093/1/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: REAL300004087093 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [153, 153, 153, 153, 201, 201, 201, 153, 69, 22, 7, 22, 1, 7, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 201, 201, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087093 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 50, 50, 115, 115, 153, 153, 142, 153, 153, 1, 2, 2, 2, 2, 2, 115, 115, 115, 115, 153, 153, 153, 153] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087093 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087093 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087093/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087093/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087093 Building REAL300004087094 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087094' /scratch/stefan/7774412/working/building/REAL300004087094 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087094 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087094/0 /scratch/stefan/7774412/working/building/REAL300004087094 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/124 `/scratch/stefan/7774412/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1) `REAL300004087094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087094 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 12, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 29, 29, 29, 17, 17, 16, 6, 17, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 17, 17, 17, 17, 29, 29, 17, 6, 6, 6, 6, 6, 1, 1, 1] 33 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087094 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 12, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 8, 17, 17, 17, 23, 23, 23, 23, 17, 17, 17, 1, 2, 2, 2, 2, 2, 3, 8, 8, 23, 23, 23, 17, 17, 17] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087094 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 12, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 11, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 23, 23, 23, 23, 33, 33, 23, 11, 11, 1, 1, 1, 6, 6, 6] 33 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 121 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087094 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087094/1 /scratch/stefan/7774412/working/building/REAL300004087094 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/125 `/scratch/stefan/7774412/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1) `REAL300004087094.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087094 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 12, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 201, 201, 201, 168, 75, 35, 7, 36, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 1, 168, 168, 168, 168, 201, 201, 7, 7, 4, 4, 4, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 12, 13, 14, 15, 16, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087094 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 12, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 33, 33, 86, 168, 168, 168, 175, 175, 175, 175, 168, 168, 168, 1, 2, 2, 2, 2, 2, 86, 86, 175, 175, 175, 168, 168, 168] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087094 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NC(C3=CC=CO3)=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 1, 1, 1, 1, 1, 12, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 201, 201, 201, 175, 99, 56, 16, 56, 4, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 175, 175, 175, 175, 201, 201, 16, 16, 1, 1, 1, 4, 4, 4] 201 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 504 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087094 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087094 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087094/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087094/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087094 Building REAL300004087095 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087095' /scratch/stefan/7774412/working/building/REAL300004087095 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087095 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087095/0 /scratch/stefan/7774412/working/building/REAL300004087095 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/126 `/scratch/stefan/7774412/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=NC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087095 none CCCOC1=CC=NC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 114, 72, 42, 42, 42, 42, 42, 12, 3, 3, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 42, 128, 128, 128, 128, 128, 114, 114, 42, 42, 12, 12, 3, 2, 2, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087095 none CCCOC1=CC=NC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 6, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 42, 42, 42, 42, 79, 109, 109, 42, 42, 42, 1, 26, 26, 26, 26, 26, 16, 16, 1, 1, 7, 7, 42, 79, 79, 42, 42, 42] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 23, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087095 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087095/1 /scratch/stefan/7774412/working/building/REAL300004087095 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/127 `/scratch/stefan/7774412/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=NC(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087095.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087095/1/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: REAL300004087095 none CCCOC1=CC=NC(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 166, 166, 154, 154, 154, 154, 154, 77, 15, 9, 15, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 154, 199, 199, 199, 199, 199, 166, 166, 154, 154, 77, 77, 3, 3, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 627 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087095 none CCCOC1=CC=NC(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 8, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 26, 26, 74, 154, 154, 154, 156, 191, 191, 154, 154, 154, 1, 8, 8, 8, 8, 8, 4, 4, 1, 1, 4, 4, 156, 156, 154, 154, 154] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 23, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087095 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087095 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087095/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087095/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087095 Building REAL300004087096 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087096' /scratch/stefan/7774412/working/building/REAL300004087096 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087096 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087096/0 /scratch/stefan/7774412/working/building/REAL300004087096 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/128 `/scratch/stefan/7774412/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CN1CCOCC1) `REAL300004087096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087096 none CC(=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 15, 20, 20, 20, 20, 20, 20, 30, 30, 30, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 20, 30, 30, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087096 none CC(=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CN1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 5, 18, 20, 20, 20, 20, 20, 5, 5, 5, 5, 2, 3, 3, 2, 2, 2, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20] 30 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087096 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087096 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087096/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087096 Building REAL300004087097 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087097' /scratch/stefan/7774412/working/building/REAL300004087097 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087097 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087097/0 /scratch/stefan/7774412/working/building/REAL300004087097 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/129 `/scratch/stefan/7774412/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=NC=CS2)S1) `REAL300004087097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087097 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 116, 116, 116, 70, 50, 50, 13, 50, 1, 13, 13, 1, 1, 1, 1, 1, 70, 70, 70, 70, 116, 116, 50, 13, 13, 13, 13, 13, 13, 1, 1] 116 rigid atoms, others: [33, 34, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 452 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087097 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 22, 22, 22, 70, 70, 70, 70, 1, 2, 2, 2, 2, 2, 2, 22, 22, 22, 23, 23, 23, 70, 70] 116 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087097 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087097/1 /scratch/stefan/7774412/working/building/REAL300004087097 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/130 `/scratch/stefan/7774412/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=NC=CS2)S1) `REAL300004087097.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087097/1/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: REAL300004087097 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 101, 101, 101, 94, 54, 48, 13, 48, 1, 13, 13, 1, 1, 1, 1, 1, 94, 94, 94, 94, 101, 101, 13, 13, 13, 13, 13, 13, 1, 1] 101 rigid atoms, others: [32, 33, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087097 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 19, 19, 52, 52, 52, 94, 94, 94, 94, 1, 2, 2, 2, 2, 2, 52, 52, 52, 52, 52, 52, 94, 94] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087097 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087097 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087097/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087097/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087097 Building REAL300004087098 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087098' /scratch/stefan/7774412/working/building/REAL300004087098 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087098 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087098/0 /scratch/stefan/7774412/working/building/REAL300004087098 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/131 `/scratch/stefan/7774412/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=C(C)C=C3)SC=N2)S1) `REAL300004087098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087098 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=C(C)C=C3)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 8, 8, 14, 27, 27, 8, 4, 4, 1, 4, 1, 1, 1, 6, 13, 13, 8, 8, 13, 13, 1, 1, 1, 7, 8, 8, 8, 14, 14, 4, 6, 13, 13, 13, 13, 13, 13, 13, 1] 39 rigid atoms, others: [40, 10, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087098 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=C(C)C=C3)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 8, 19, 27, 27, 24, 24, 27, 27, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 19, 27, 27, 27, 27, 27, 27, 27, 7] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087098 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=C(C)C=C3)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 5, 1, 1, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 39, 39, 39, 27, 23, 23, 13, 23, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 27, 27, 27, 27, 39, 39, 23, 6, 1, 1, 2, 2, 2, 1, 1, 13] 39 rigid atoms, others: [33, 34, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087098 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087098 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087098/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087098 Building REAL300004087099 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087099' /scratch/stefan/7774412/working/building/REAL300004087099 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087099 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087099/0 /scratch/stefan/7774412/working/building/REAL300004087099 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/132 `/scratch/stefan/7774412/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CC=C3C)SC=N2)S1) `REAL300004087099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087099 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CC=C3C)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [8, 9, 9, 9, 15, 27, 27, 9, 6, 6, 1, 6, 1, 1, 1, 6, 17, 17, 17, 17, 17, 17, 1, 1, 1, 9, 9, 9, 9, 15, 15, 6, 6, 17, 17, 17, 17, 17, 17, 17, 1] 63 rigid atoms, others: [40, 10, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087099 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CC=C3C)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 25, 40, 40, 40, 40, 40, 40, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 25, 40, 40, 40, 40, 40, 40, 40, 9] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087099 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(NC3=CC=CC=C3C)SC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 63, 63, 63, 40, 35, 35, 17, 35, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 40, 40, 40, 40, 63, 63, 35, 7, 1, 1, 1, 1, 2, 2, 2, 17] 63 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087099 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087099 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087099/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087099 Building REAL300004087100 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087100' /scratch/stefan/7774412/working/building/REAL300004087100 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087100 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087100/0 /scratch/stefan/7774412/working/building/REAL300004087100 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/133 `/scratch/stefan/7774412/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C3=CC=CN=C23)S1) `REAL300004087100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087100 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C3=CC=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 8, 1, 1, 2, 2, 2, 1, 1, 1] 19 rigid atoms, others: [35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 77 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087100 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C3=CC=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087100 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087100 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087100/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087100 Building REAL300004087101 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087101' /scratch/stefan/7774412/working/building/REAL300004087101 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087101 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087101/0 /scratch/stefan/7774412/working/building/REAL300004087101 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/134 `/scratch/stefan/7774412/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=C(F)C=C2)S1) `REAL300004087101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087101 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 1, 1, 1, 1] 15 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087101 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087101 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087101 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087101/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087101 Building REAL300004087102 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087102' /scratch/stefan/7774412/working/building/REAL300004087102 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087102 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087102/0 /scratch/stefan/7774412/working/building/REAL300004087102 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/135 `/scratch/stefan/7774412/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCC1) `REAL300004087102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087102 none C=CC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 61 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087102 none C=CC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 9, 18, 18, 19, 31, 31, 31, 61, 61, 61, 31, 31, 31, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 19, 61, 61, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 61 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 40, 41, 42, 39, 34, 17, 18, 19, 20, 21, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087102 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087102 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087102/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087102 Building REAL300004087103 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087103' /scratch/stefan/7774412/working/building/REAL300004087103 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087103 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087103/0 /scratch/stefan/7774412/working/building/REAL300004087103 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/136 `/scratch/stefan/7774412/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=C(Cl)C=C2)S1) `REAL300004087103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087103 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 1, 1, 1, 1] 15 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087103 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087103 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087103 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087103/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087103 Building REAL300004087104 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087104' /scratch/stefan/7774412/working/building/REAL300004087104 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087104 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087104/0 /scratch/stefan/7774412/working/building/REAL300004087104 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/137 `/scratch/stefan/7774412/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087104 none CCCCNC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 117, 73, 32, 15, 15, 15, 5, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 133, 133, 133, 133, 133, 117, 117, 73, 73, 32, 15, 14, 15, 15, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 640 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087104 none CCCCNC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 26, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 15, 15, 15, 28, 50, 50, 15, 15, 15, 40, 40, 40, 40, 40, 26, 26, 14, 14, 4, 1, 1, 1, 1, 14, 28, 28, 15, 15, 15] 201 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087104 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087104 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087104/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087104 Building REAL300004087105 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087105' /scratch/stefan/7774412/working/building/REAL300004087105 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087105 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087105/0 /scratch/stefan/7774412/working/building/REAL300004087105 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/138 `/scratch/stefan/7774412/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCNC2=CC=CC=C2C)S1) `REAL300004087105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087105 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCNC2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 28, 28, 28, 19, 19, 18, 18, 18, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 28, 28, 19, 18, 18, 13, 13, 3, 1, 1, 1, 1, 2, 2, 2] 28 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087105 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCNC2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 2, 4, 17, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 17, 19, 19, 19, 19, 19, 19, 19] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087105 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087105 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087105/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087105 Building REAL300004087106 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087106' /scratch/stefan/7774412/working/building/REAL300004087106 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087106 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087106/0 /scratch/stefan/7774412/working/building/REAL300004087106 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/139 `/scratch/stefan/7774412/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CCCC(C2)C3=O)S1) `REAL300004087106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087106 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CCCC(C2)C3=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 23, 23, 23, 18, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 23, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087106 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CCCC(C2)C3=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087106 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087106 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087106/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087106 Building REAL300004087107 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087107' /scratch/stefan/7774412/working/building/REAL300004087107 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087107 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087107/0 /scratch/stefan/7774412/working/building/REAL300004087107 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/140 `/scratch/stefan/7774412/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(O)C=C2)S1) `REAL300004087107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087107 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 12, 12, 12, 10, 10, 10, 3, 10, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 3, 3, 1, 1, 2, 1, 1] 24 rigid atoms, others: [33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 39 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: REAL300004087107 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 10, 10, 7, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 7, 7, 10, 10, 20, 10, 10] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087107 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087107 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087107/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087107 Building REAL300004087108 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087108' /scratch/stefan/7774412/working/building/REAL300004087108 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087108 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087108/0 /scratch/stefan/7774412/working/building/REAL300004087108 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/141 `/scratch/stefan/7774412/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C([O-])C(Cl)=C2)S1) `REAL300004087108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087108 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C([O-])C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 7, 1, 1, 1] 21 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087108 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C([O-])C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 2, 2, 2, 11, 11, 9, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087108 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087108/1 /scratch/stefan/7774412/working/building/REAL300004087108 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/142 `/scratch/stefan/7774412/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(O)C(Cl)=C2)S1) `REAL300004087108.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087108/1/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: REAL300004087108 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(O)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 12, 12, 12, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 7, 1, 1, 2, 1] 24 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087108 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(O)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 5, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 14, 7] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087108 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087108 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087108/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087108/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087108 Building REAL300004087109 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087109' /scratch/stefan/7774412/working/building/REAL300004087109 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087109 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087109/0 /scratch/stefan/7774412/working/building/REAL300004087109 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/143 `/scratch/stefan/7774412/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(C)C)=CC(C(C)C)=C2O)S1) `REAL300004087109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087109 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(C)C)=CC(C(C)C)=C2O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 5, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [20, 21, 21, 21, 37, 47, 47, 21, 14, 12, 1, 12, 1, 1, 1, 1, 4, 4, 1, 1, 1, 2, 2, 1, 1, 21, 21, 21, 21, 37, 37, 14, 1, 4, 5, 5, 5, 5, 5, 5, 1, 2, 3, 3, 3, 2, 2, 2, 2] 136 rigid atoms, others: [32, 40, 10, 12, 13, 14, 15, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 228 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087109 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(C)C)=CC(C(C)C)=C2O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 1, 1, 5, 5, 5, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 21, 21, 21, 40, 40, 6, 21, 21, 35, 35, 21, 21, 1, 2, 2, 2, 2, 2, 2, 21, 40, 40, 40, 40, 40, 40, 40, 20, 35, 35, 35, 35, 35, 35, 35, 42] 136 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 324 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087109 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087109 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087109/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087109 Building REAL300004087110 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087110' /scratch/stefan/7774412/working/building/REAL300004087110 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087110 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087110/0 /scratch/stefan/7774412/working/building/REAL300004087110 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/144 `/scratch/stefan/7774412/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CO)C=C2)S1) `REAL300004087110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087110 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CO)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 13, 17, 17, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 8, 8, 24, 1, 1] 81 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087110 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CO)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 3, 3, 23, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 23, 23, 69, 7, 7] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087110 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087110 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087110/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087110 Building REAL300004087111 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087111' /scratch/stefan/7774412/working/building/REAL300004087111 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087111 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087111/0 /scratch/stefan/7774412/working/building/REAL300004087111 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/145 `/scratch/stefan/7774412/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCNS(=O)(=O)C2=CC=CS2)S1) `REAL300004087111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087111 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCNS(=O)(=O)C2=CC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 155, 155, 155, 119, 119, 119, 119, 119, 83, 21, 6, 1, 6, 6, 1, 1, 1, 1, 1, 119, 119, 119, 119, 155, 155, 119, 119, 119, 83, 83, 21, 1, 1, 1] 155 rigid atoms, others: [35, 36, 37, 15, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 721 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087111 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCNS(=O)(=O)C2=CC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 4, 18, 57, 57, 57, 119, 119, 119, 119, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 18, 119, 119, 119] 155 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087111 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087111 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087111/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087111 Building REAL300004087112 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087112' /scratch/stefan/7774412/working/building/REAL300004087112 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087112 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087112/0 /scratch/stefan/7774412/working/building/REAL300004087112 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/146 `/scratch/stefan/7774412/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(Cl)=C1O) `REAL300004087112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087112 none CCOC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 11, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 11, 2, 2, 2, 2, 2, 2, 11, 22] 86 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087112 none CCOC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(Cl)=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 30, 30, 11, 11, 11, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 7, 21, 21, 11, 11, 11, 1, 2] 86 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 144 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087112 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087112/1 /scratch/stefan/7774412/working/building/REAL300004087112 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/147 `/scratch/stefan/7774412/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(Cl)=C1[O-]) `REAL300004087112.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087112/1/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: REAL300004087112 none CCOC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 3, 2, 2, 2, 2, 2, 2, 3] 16 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087112 none CCOC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 3, 5, 5, 3, 3, 3, 1] 16 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 36, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087112 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087112 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087112/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087112/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087112 Building REAL300004087113 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087113' /scratch/stefan/7774412/working/building/REAL300004087113 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087113 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087113/0 /scratch/stefan/7774412/working/building/REAL300004087113 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/148 `/scratch/stefan/7774412/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2N=C1CC) `REAL300004087113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087113 none CCC1=NC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2N=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 13, 13, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 13, 13, 13, 43, 39, 39, 39, 39, 39, 13, 13, 2, 2, 2, 2, 2, 2, 13, 43, 43, 43, 43, 43] 83 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 288 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087113 none CCC1=NC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2N=C1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 31, 31, 13, 13, 13, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 9, 25, 25, 13, 13, 13, 1, 6, 6, 6, 6, 6] 83 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 40, 21, 22, 23, 24, 25, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087113 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087113 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087113/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087113 Building REAL300004087114 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087114' /scratch/stefan/7774412/working/building/REAL300004087114 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087114 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087114/0 /scratch/stefan/7774412/working/building/REAL300004087114 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/149 `/scratch/stefan/7774412/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2OCC2=CC=CC=C2C)S1) `REAL300004087114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087114 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2OCC2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 11, 25, 25, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 10, 40, 103, 103, 66, 103, 103, 103, 6, 6, 6, 6, 11, 11, 6, 1, 1, 1, 1, 40, 40, 103, 103, 67, 103, 103, 103, 103] 201 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 381 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087114 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2OCC2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 27, 86, 149, 149, 124, 149, 149, 149, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 86, 86, 149, 149, 124, 149, 149, 149, 149] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 472 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087114 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2OCC2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 201, 201, 201, 149, 149, 149, 103, 149, 103, 103, 101, 103, 103, 31, 7, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 201, 201, 149, 103, 103, 103, 103, 7, 7, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [40, 41, 42, 43, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 643 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087114 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087114 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087114/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087114 Building REAL300004087115 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087115' /scratch/stefan/7774412/working/building/REAL300004087115 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087115 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087115/0 /scratch/stefan/7774412/working/building/REAL300004087115 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/150 `/scratch/stefan/7774412/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1NCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087115 none COC1=CC=C(Cl)C=C1NCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 20, 20, 10, 20, 20, 20, 10, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 26, 26, 26, 20, 11, 20, 10, 2, 2, 2, 2, 2, 2, 2, 2] 32 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 104 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087115 none COC1=CC=C(Cl)C=C1NCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 19, 19, 19, 20, 20, 20, 20, 28, 32, 32, 20, 20, 20, 3, 3, 3, 1, 1, 1, 3, 19, 19, 20, 28, 28, 20, 20, 20] 32 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 135 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087115 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087115/1 /scratch/stefan/7774412/working/building/REAL300004087115 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/151 `/scratch/stefan/7774412/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(Cl)C=C1NCC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087115.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087115/1/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: REAL300004087115 none COC1=CC=C(Cl)C=C1NCC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 139, 139, 139, 108, 139, 139, 139, 108, 96, 46, 13, 46, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 169, 169, 169, 137, 108, 139, 108, 96, 96, 2, 2, 2, 2, 2] 201 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087115 none COC1=CC=C(Cl)C=C1NCC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 21, 21, 57, 139, 139, 139, 173, 201, 201, 139, 139, 139, 4, 4, 4, 1, 1, 1, 3, 5, 5, 173, 173, 139, 139, 139] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087115 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087115 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087115/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087115/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087115 Building REAL300004087116 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087116' /scratch/stefan/7774412/working/building/REAL300004087116 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087116 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087116/0 /scratch/stefan/7774412/working/building/REAL300004087116 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/152 `/scratch/stefan/7774412/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC[NH+]1CCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC1) `REAL300004087116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087116 none C#CC[NH+]1CCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 3, 3, 7, 7, 7, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 11 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087116 none C#CC[NH+]1CCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 3, 5, 5, 3, 3, 3, 1, 1, 1, 1] 11 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 38, 39, 40, 21, 22, 26, 27, 28, 29, 30, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 31, 32, 33, 34, 35, 36]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087116 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087116 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087116/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087116 Building REAL300004087117 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087117' /scratch/stefan/7774412/working/building/REAL300004087117 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087117 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087117/0 /scratch/stefan/7774412/working/building/REAL300004087117 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/153 `/scratch/stefan/7774412/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087117 none COCCOC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 23, 8, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 27, 27, 27, 24, 24, 23, 23, 3, 3, 3, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087117 none COCCOC1=NC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 21, 19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 8, 8, 3, 3, 3, 24, 24, 24, 21, 21, 19, 19, 1, 1, 1, 3, 5, 5, 3, 3, 3] 27 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087117 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087117 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087117/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087117 Building REAL300004087118 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087118' /scratch/stefan/7774412/working/building/REAL300004087118 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087118 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087118/0 /scratch/stefan/7774412/working/building/REAL300004087118 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/154 `/scratch/stefan/7774412/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1CCCCC1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087118 none CCCN1CCCCC1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 10, 10, 10, 10, 10, 10, 4, 3, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 21, 21, 21, 21, 21, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 2, 2, 1, 1, 1] 37 rigid atoms, others: [43, 41, 42, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 113 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087118 none CCCN1CCCCC1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 10, 10, 10, 19, 28, 28, 10, 10, 10, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 19, 10, 10, 10] 37 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087118 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087118 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087118/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087118 Building REAL300004087119 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087119' /scratch/stefan/7774412/working/building/REAL300004087119 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087119 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087119/0 /scratch/stefan/7774412/working/building/REAL300004087119 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/155 `/scratch/stefan/7774412/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C[NH+](C)C)S1) `REAL300004087119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087119 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C[NH+](C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087119 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C[NH+](C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 9, 6, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 3, 3, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087119 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087119 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087119/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087119 Building REAL300004087120 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087120' /scratch/stefan/7774412/working/building/REAL300004087120 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087120 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087120/0 /scratch/stefan/7774412/working/building/REAL300004087120 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/156 `/scratch/stefan/7774412/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC3CC3)N=C2)S1) `REAL300004087120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087120 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC3CC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 47, 47, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 5, 21, 61, 61, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 21, 21, 61, 61, 61, 61, 61, 1] 201 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087120 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC3CC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 36, 91, 144, 144, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 91, 91, 144, 144, 144, 144, 144, 13] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087120 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC3CC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 201, 201, 201, 144, 127, 123, 61, 123, 61, 61, 61, 40, 10, 1, 1, 1, 1, 61, 61, 144, 144, 144, 144, 201, 201, 127, 61, 61, 10, 10, 1, 1, 1, 1, 1, 61] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 672 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087120 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087120 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087120/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087120 Building REAL300004087121 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087121' /scratch/stefan/7774412/working/building/REAL300004087121 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087121 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087121/0 /scratch/stefan/7774412/working/building/REAL300004087121 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/157 `/scratch/stefan/7774412/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+]1CCN(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC1) `REAL300004087121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087121 none CC[NH+]1CCN(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 10, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 13, 13, 13, 13, 13, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 20, 20, 20, 20, 20, 13, 13, 13, 13, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 20 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 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: 95 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087121 none CC[NH+]1CCN(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 10, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 13, 13, 13, 13, 13, 13, 16, 20, 20, 13, 13, 13, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 10, 10, 10, 10, 13, 16, 16, 13, 13, 13, 1, 1, 1, 1] 20 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 43, 44, 45, 46, 22, 23, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087121 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087121 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087121/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087121 Building REAL300004087122 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087122' /scratch/stefan/7774412/working/building/REAL300004087122 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087122 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087122/0 /scratch/stefan/7774412/working/building/REAL300004087122 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/158 `/scratch/stefan/7774412/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C=C([O-])C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)C=C1) `REAL300004087122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087122 none COC1=CC=C(N2C=C([O-])C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.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, 8, 1, 1, 12, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 15, 33, 33, 9, 9, 9, 1, 6, 6, 6, 6, 6, 6, 6, 1, 6, 15, 15, 9, 9, 9, 6, 6] 35 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 24] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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: REAL300004087122 none COC1=CC=C(N2C=C([O-])C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.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, 8, 1, 1, 12, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 17, 17, 17, 25, 25, 25, 35, 35, 35, 25, 25, 25, 6, 1, 1, 1, 1, 1, 1, 1, 6, 17, 35, 35, 25, 25, 25, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087122 none COC1=CC=C(N2C=C([O-])C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.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, 8, 1, 1, 12, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 17, 25, 25, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 25, 25, 25, 25, 25, 25, 25, 9, 2, 2, 2, 2, 2, 2, 25, 25] 35 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087122 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087122 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087122/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087122 Building REAL300004087123 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087123' /scratch/stefan/7774412/working/building/REAL300004087123 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL300004087123 as failed and skipping /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `/scratch/stefan/7774412/failed' `/scratch/stefan/7774412/working/building/REAL300004087123' -> `/scratch/stefan/7774412/failed/REAL300004087123' Building REAL300004087124 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087124' /scratch/stefan/7774412/working/building/REAL300004087124 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087124 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087124/0 /scratch/stefan/7774412/working/building/REAL300004087124 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/159 `/scratch/stefan/7774412/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N(C)C)S1) `REAL300004087124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087124 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 36, 38, 38, 19, 15, 14, 4, 14, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 19, 19, 19, 19, 36, 36, 15, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 40 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087124 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 14, 19, 19, 17, 19, 19, 14, 20, 20, 1, 2, 2, 2, 2, 2, 2, 14, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 20] 40 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087124 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087124 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087124/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087124 Building REAL300004087125 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087125' /scratch/stefan/7774412/working/building/REAL300004087125 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087125 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087125/0 /scratch/stefan/7774412/working/building/REAL300004087125 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/160 `/scratch/stefan/7774412/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC2=NC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C12) `REAL300004087125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087125 none CCC1=NOC2=NC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [27, 13, 13, 13, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 27, 27, 27, 27, 27, 13, 2, 2, 2, 2, 2, 2, 13] 49 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087125 none CCC1=NOC2=NC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 27, 27, 13, 13, 13, 1, 1, 5, 5, 5, 4, 4, 1, 9, 25, 25, 13, 13, 13, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 36, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087125 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087125 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087125/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087125 Building REAL300004087126 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087126' /scratch/stefan/7774412/working/building/REAL300004087126 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087126 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087126/0 /scratch/stefan/7774412/working/building/REAL300004087126 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/161 `/scratch/stefan/7774412/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CN=C2)S1) `REAL300004087126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087126 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 27, 49, 72, 72, 27, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 26, 27, 27, 27, 49, 49, 14, 1, 2, 2, 2, 11, 11, 11, 11] 105 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 298 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087126 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 26, 26, 26, 26, 26, 27, 67, 67, 67, 67, 67, 1, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 67, 67, 67, 67] 105 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087126 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 105, 105, 105, 67, 51, 49, 11, 49, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 105, 105, 51, 11, 11, 11, 11, 1, 1, 1, 1] 105 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 376 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087126 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087126 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087126/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087126 Building REAL300004087127 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087127' /scratch/stefan/7774412/working/building/REAL300004087127 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087127 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087127/0 /scratch/stefan/7774412/working/building/REAL300004087127 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/162 `/scratch/stefan/7774412/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC(C(C)C)=N2)S1) `REAL300004087127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087127 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC(C(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [15, 16, 16, 16, 28, 44, 44, 16, 13, 13, 1, 13, 1, 1, 1, 1, 1, 13, 13, 1, 16, 16, 16, 16, 28, 28, 13, 1, 1, 13, 13, 13, 13, 13, 13, 13] 55 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087127 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC(C(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 42, 42, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 42, 42, 42, 42, 42, 42, 42] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087127 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087127 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087127/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087127 Building REAL300004087128 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087128' /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087128 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087128/0 /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/163 `/scratch/stefan/7774412/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1) `REAL300004087128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 4, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 3, 3, 3, 3, 4, 4, 3, 6, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1] 30 rigid atoms, others: [34, 35, 36, 37, 10, 45, 12, 13, 14, 15, 16, 17, 18, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 3, 1, 2, 2, 2, 2, 2, 2, 9, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 3, 3] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 10, 10, 10, 8, 8, 8, 7, 8, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 10, 10, 8, 21, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7] 30 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 57 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087128/1 /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/164 `/scratch/stefan/7774412/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1) `REAL300004087128.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087128/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1] 9 rigid atoms, others: [34, 35, 36, 37, 10, 45, 12, 13, 14, 15, 16, 17, 18, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 2, 1, 2, 2, 2, 2, 2, 2, 6, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 3, 3] 9 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46]) total number of confs: 20 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087128/2 /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/165 `/scratch/stefan/7774412/working/3D/165' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1) `REAL300004087128.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087128/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 26, 30, 30, 26, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 1, 26, 26, 26, 26, 26, 26, 6, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 1, 1] 132 rigid atoms, others: [33, 34, 35, 36, 44, 10, 45, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 9, 18, 18, 26, 26, 26, 26, 26, 26, 44, 44, 44, 44, 44, 44, 26, 1, 2, 2, 2, 2, 2, 78, 26, 26, 26, 26, 44, 44, 44, 44, 44, 44, 44, 26, 26] 132 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 27, 22, 7, 22, 7, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 7, 44, 44, 44, 44, 44, 44, 21, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 7, 7] 132 rigid atoms, others: [39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 118 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087128/3 /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/166 `/scratch/stefan/7774412/working/3D/166' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1) `REAL300004087128.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087128/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 6, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1] 9 rigid atoms, others: [33, 34, 35, 36, 44, 10, 45, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087128 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC[N@@H+](CC3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 6, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2] 9 rigid atoms, others: [39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45]) total number of confs: 17 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087128 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087128 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087128/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087128/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087128/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087128/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087128 Building REAL300004087129 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087129' /scratch/stefan/7774412/working/building/REAL300004087129 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087129 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087129/0 /scratch/stefan/7774412/working/building/REAL300004087129 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/167 `/scratch/stefan/7774412/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C(C)C)S1) `REAL300004087129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087129 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 72, 77, 77, 37, 26, 24, 10, 24, 6, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 37, 37, 37, 37, 72, 72, 26, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20] 88 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 380 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087129 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 17, 31, 37, 37, 37, 37, 37, 17, 33, 35, 1, 2, 2, 2, 2, 2, 2, 17, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 35, 35, 35, 35, 35, 35, 35] 88 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 266 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087129 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087129 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087129/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087129 Building REAL300004087130 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087130' /scratch/stefan/7774412/working/building/REAL300004087130 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087130 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087130/0 /scratch/stefan/7774412/working/building/REAL300004087130 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/168 `/scratch/stefan/7774412/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC3=CC=NC=C3)=C2)S1) `REAL300004087130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087130 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC3=CC=NC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 29, 29, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 19, 19, 11, 19, 19, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 19, 19, 19, 19, 1] 201 rigid atoms, others: [32, 33, 34, 39, 10, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087130 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC3=CC=NC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 87, 109, 109, 87, 109, 109, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 109, 109, 109, 109, 13] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087130 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC3=CC=NC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 201, 201, 201, 109, 71, 67, 19, 67, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 109, 109, 109, 109, 201, 201, 71, 19, 19, 19, 1, 1, 1, 1, 19] 201 rigid atoms, others: [35, 36, 37, 38, 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, 39]) total number of confs: 784 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087130 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087130 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087130/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087130 Building REAL300004087131 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087131' /scratch/stefan/7774412/working/building/REAL300004087131 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087131 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087131/0 /scratch/stefan/7774412/working/building/REAL300004087131 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/169 `/scratch/stefan/7774412/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC(C)C)S1) `REAL300004087131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087131 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 31, 49, 49, 16, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 16, 16, 16, 16, 31, 31, 14, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13] 61 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087131 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2NC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 16, 16, 30, 39, 39, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 30, 39, 39, 39, 39, 39, 39, 39] 61 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087131 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087131 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087131/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087131 Building REAL300004087132 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087132' /scratch/stefan/7774412/working/building/REAL300004087132 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087132 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087132/0 /scratch/stefan/7774412/working/building/REAL300004087132 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/170 `/scratch/stefan/7774412/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1) `REAL300004087132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087132 none CC1=NC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 16, 8, 2, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 39, 39, 39, 39, 39, 16, 16, 8, 8, 2, 2, 2, 2, 2, 2, 39] 64 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087132 none CC1=NC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 15, 35, 35, 39, 39, 39, 39, 64, 64, 64, 39, 39, 39, 1, 1, 2, 2, 2, 7, 7, 15, 15, 39, 64, 64, 39, 39, 39, 1] 64 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087132 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087132 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087132/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087132 Building REAL300004087133 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087133' /scratch/stefan/7774412/working/building/REAL300004087133 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087133 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087133/0 /scratch/stefan/7774412/working/building/REAL300004087133 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/171 `/scratch/stefan/7774412/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CNC(C2=CC=CC=C2)C(F)(F)F)S1) `REAL300004087133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087133 none CC1=C(CC(=O)[O-])N=C(NC(=O)CNC(C2=CC=CC=C2)C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 19, 19, 19, 17, 17, 17, 16, 17, 6, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 17, 17, 17, 17, 19, 19, 17, 16, 16, 6, 3, 1, 1, 1, 1, 1] 19 rigid atoms, others: [36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087133 none CC1=C(CC(=O)[O-])N=C(NC(=O)CNC(C2=CC=CC=C2)C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 3, 7, 14, 17, 17, 14, 17, 17, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 3, 3, 7, 14, 17, 17, 17, 17, 17] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087133 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087133/1 /scratch/stefan/7774412/working/building/REAL300004087133 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/172 `/scratch/stefan/7774412/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNC(C2=CC=CC=C2)C(F)(F)F)S1) `REAL300004087133.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087133/1/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: REAL300004087133 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNC(C2=CC=CC=C2)C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 79, 34, 12, 34, 4, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 167, 167, 167, 167, 201, 201, 12, 12, 4, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL300004087133 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNC(C2=CC=CC=C2)C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 46, 46, 132, 159, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 1, 2, 2, 2, 2, 2, 132, 132, 159, 167, 167, 167, 167, 167, 167] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087133 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087133 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087133/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087133/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087133 Building REAL300004087134 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087134' /scratch/stefan/7774412/working/building/REAL300004087134 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087134 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087134/0 /scratch/stefan/7774412/working/building/REAL300004087134 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/173 `/scratch/stefan/7774412/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CN=C2C(C)C)S1) `REAL300004087134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087134 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CN=C2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 43, 43, 43, 24, 24, 22, 10, 22, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 43, 43, 24, 10, 10, 6, 6, 1, 1, 5, 6, 6, 6, 5, 5, 5] 47 rigid atoms, others: [33, 34, 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, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087134 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CN=C2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 10, 12, 24, 24, 24, 24, 24, 28, 28, 1, 2, 2, 2, 2, 2, 2, 10, 10, 12, 12, 24, 24, 28, 28, 28, 28, 28, 28, 28] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087134 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087134/1 /scratch/stefan/7774412/working/building/REAL300004087134 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/174 `/scratch/stefan/7774412/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=C[NH+]=C2C(C)C)S1) `REAL300004087134.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087134/1/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: REAL300004087134 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=C[NH+]=C2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 8, 6, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 19, 23, 23, 14, 14, 14, 10, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 14, 14, 19, 19, 14, 10, 10, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6] 27 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087134 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=C[NH+]=C2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 8, 6, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 8, 14, 14, 14, 14, 14, 14, 22, 22, 1, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 14, 14, 22, 22, 22, 22, 22, 22, 22] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087134 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087134 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087134/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087134/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087134 Building REAL300004087135 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087135' /scratch/stefan/7774412/working/building/REAL300004087135 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087135 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087135/0 /scratch/stefan/7774412/working/building/REAL300004087135 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/175 `/scratch/stefan/7774412/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C[NH+](C)C)C3=CC=CC=C3O2)S1) `REAL300004087135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087135 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C[NH+](C)C)C3=CC=CC=C3O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 11, 15, 15, 10, 9, 9, 1, 9, 1, 1, 1, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 11, 11, 9, 6, 6, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 15 rigid atoms, others: [41, 10, 43, 12, 13, 14, 44, 19, 20, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087135 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C[NH+](C)C)C3=CC=CC=C3O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 9, 6, 5, 5, 1, 1, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 10, 10, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087135 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087135 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087135/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087135 Building REAL300004087136 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087136' /scratch/stefan/7774412/working/building/REAL300004087136 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087136 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087136/0 /scratch/stefan/7774412/working/building/REAL300004087136 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/176 `/scratch/stefan/7774412/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Br)=CN=C2N(C)C)S1) `REAL300004087136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087136 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Br)=CN=C2N(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 27, 27, 14, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 26, 26, 11, 1, 1, 4, 4, 4, 4, 4, 4] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087136 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Br)=CN=C2N(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 17, 1, 8, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 17, 17, 1, 2, 2, 2, 2, 2, 2, 14, 14, 17, 17, 17, 17, 17, 17] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087136 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087136 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087136/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087136 Building REAL300004087137 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087137' /scratch/stefan/7774412/working/building/REAL300004087137 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087137 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087137/0 /scratch/stefan/7774412/working/building/REAL300004087137 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/177 `/scratch/stefan/7774412/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(O)CCCCC2)S1) `REAL300004087137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087137 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(O)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 17, 17, 17, 11, 11, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 11, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 74 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087137 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(O)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 9, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 9, 9, 33, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087137 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087137 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087137/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087137 Building REAL300004087138 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087138' /scratch/stefan/7774412/working/building/REAL300004087138 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087138 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087138/0 /scratch/stefan/7774412/working/building/REAL300004087138 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/178 `/scratch/stefan/7774412/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(NC3=CC=CC=C3)=C2)S1) `REAL300004087138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087138 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(NC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 44, 44, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 13, 42, 42, 16, 42, 42, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 13, 42, 42, 20, 42, 42, 1] 201 rigid atoms, others: [32, 33, 34, 41, 10, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087138 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(NC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 87, 124, 124, 89, 124, 124, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 87, 124, 124, 114, 124, 124, 13] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087138 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(NC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 201, 201, 201, 124, 111, 108, 42, 108, 42, 42, 42, 42, 7, 1, 1, 1, 1, 1, 1, 1, 42, 124, 124, 124, 124, 201, 201, 111, 42, 42, 42, 7, 1, 1, 1, 1, 1, 42] 201 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 748 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087138 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087138 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087138/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087138 Building REAL300004087139 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087139' /scratch/stefan/7774412/working/building/REAL300004087139 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087139 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087139/0 /scratch/stefan/7774412/working/building/REAL300004087139 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/179 `/scratch/stefan/7774412/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2(C)NC(=O)NC2=O)S1) `REAL300004087139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087139 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2(C)NC(=O)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 24, 24, 24, 15, 15, 15, 11, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 24, 24, 15, 11, 11, 7, 7, 7, 7, 2, 2, 2, 1, 1] 24 rigid atoms, others: [39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087139 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2(C)NC(=O)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 8, 8, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 5, 5, 8, 8, 8, 8, 15, 15, 15, 15, 15] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087139 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087139 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087139/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087139 Building REAL300004087140 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087140' /scratch/stefan/7774412/working/building/REAL300004087140 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087140 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087140/0 /scratch/stefan/7774412/working/building/REAL300004087140 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/180 `/scratch/stefan/7774412/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)C)N=C2)S1) `REAL300004087140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087140 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 27, 27, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 5, 5, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1] 37 rigid atoms, others: [37, 10, 12, 13, 14, 15, 16, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087140 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 23, 23, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 23, 23, 23, 23, 23, 23, 23, 13] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087140 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087140 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087140/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087140 Building REAL300004087141 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087141' /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087141 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087141/0 /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/181 `/scratch/stefan/7774412/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2C2CCCC2)S1) `REAL300004087141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 19, 19, 19, 18, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 18, 18, 18, 18, 19, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 20 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 42 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 1, 2, 2, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19] 20 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 20, 20, 20, 19, 11, 6, 2, 6, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 19, 19, 19, 19, 20, 20, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087141/1 /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/182 `/scratch/stefan/7774412/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2C2CCCC2)S1) `REAL300004087141.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 17, 17, 17, 16, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 16, 16, 16, 16, 17, 17, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 17 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 17, 17, 17, 16, 11, 6, 3, 6, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 16, 16, 16, 16, 17, 17, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087141/2 /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/183 `/scratch/stefan/7774412/working/3D/183' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2C2CCCC2)S1) `REAL300004087141.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087141/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 11 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 23, 27, 28] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 19 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 7 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087141/3 /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/184 `/scratch/stefan/7774412/working/3D/184' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2C2CCCC2)S1) `REAL300004087141.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087141/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 2, 2, 2, 2, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087141 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 19 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087141 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087141 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087141/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087141/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087141/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087141/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087141 Building REAL300004087142 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087142' /scratch/stefan/7774412/working/building/REAL300004087142 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087142 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087142/0 /scratch/stefan/7774412/working/building/REAL300004087142 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/185 `/scratch/stefan/7774412/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN3C=NC=C3C2)S1) `REAL300004087142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087142 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN3C=NC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 12, 12, 12, 8, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087142 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN3C=NC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 8, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8] 12 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087142 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087142 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087142/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087142 Building REAL300004087143 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087143' /scratch/stefan/7774412/working/building/REAL300004087143 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087143 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087143/0 /scratch/stefan/7774412/working/building/REAL300004087143 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/186 `/scratch/stefan/7774412/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=C(Cl)C(F)=C2)S1) `REAL300004087143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087143 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=C(Cl)C(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 46, 46, 46, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 46, 46, 29, 29, 29, 1, 1, 1] 46 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 192 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087143 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=C(Cl)C(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 2, 10, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 2, 2, 2, 29, 29, 29] 46 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087143 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087143/1 /scratch/stefan/7774412/working/building/REAL300004087143 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/187 `/scratch/stefan/7774412/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=C(Cl)C(F)=C2)S1) `REAL300004087143.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087143/1/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: REAL300004087143 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=C(Cl)C(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 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: [165, 165, 165, 165, 201, 201, 201, 165, 106, 62, 25, 61, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 201, 201, 25, 25, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 564 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087143 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=C(Cl)C(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 28, 28, 55, 127, 165, 165, 165, 165, 165, 165, 165, 1, 2, 2, 2, 2, 2, 55, 55, 165, 165, 165] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 404 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087143 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087143 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087143/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087143/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087143 Building REAL300004087144 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087144' /scratch/stefan/7774412/working/building/REAL300004087144 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087144 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087144/0 /scratch/stefan/7774412/working/building/REAL300004087144 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/188 `/scratch/stefan/7774412/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NN=CN3)C=C2)S1) `REAL300004087144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087144 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NN=CN3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 9, 9, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 1, 1, 4, 4, 4, 4, 7, 7, 4, 1, 1, 8, 8, 13, 13, 1, 1] 17 rigid atoms, others: [32, 37, 38, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087144 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NN=CN3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 13, 15, 15, 15, 15, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 13, 13, 15, 15, 4, 4] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087144 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NN=CN3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 17, 17, 17, 15, 15, 15, 13, 15, 9, 13, 13, 6, 1, 1, 1, 1, 1, 1, 13, 13, 15, 15, 15, 15, 17, 17, 15, 13, 13, 6, 6, 1, 1, 13, 13] 17 rigid atoms, others: [35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087144 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087144/1 /scratch/stefan/7774412/working/building/REAL300004087144 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/189 `/scratch/stefan/7774412/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NNC=N3)C=C2)S1) `REAL300004087144.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087144 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NNC=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 13, 29, 29, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 8, 48, 48, 48, 48, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 8, 8, 48, 48, 1, 1] 201 rigid atoms, others: [32, 37, 38, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087144 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NNC=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 3, 3, 39, 110, 110, 110, 110, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 39, 39, 110, 110, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087144 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3=NNC=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 8, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 201, 201, 201, 110, 82, 74, 19, 74, 19, 48, 48, 9, 1, 1, 1, 1, 1, 1, 48, 48, 110, 110, 110, 110, 201, 201, 82, 48, 48, 9, 9, 1, 1, 48, 48] 201 rigid atoms, others: [35, 36, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 892 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087144 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087144 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087144/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087144/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087144 Building REAL300004087145 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087145' /scratch/stefan/7774412/working/building/REAL300004087145 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087145 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087145/0 /scratch/stefan/7774412/working/building/REAL300004087145 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/190 `/scratch/stefan/7774412/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC(S(N)(=O)=O)=C2)S1) `REAL300004087145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087145 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC(S(N)(=O)=O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 14, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 5, 4, 4, 1, 11, 11, 11, 11, 21, 21, 7, 1, 5, 5, 1] 73 rigid atoms, others: [10, 12, 13, 14, 15, 16, 20, 28, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087145 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC(S(N)(=O)=O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 14, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 39, 39, 39, 11, 1, 2, 2, 2, 2, 2, 2, 11, 39, 39, 11] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087145 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087145 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087145/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087145 Building REAL300004087146 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087146' /scratch/stefan/7774412/working/building/REAL300004087146 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087146 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087146/0 /scratch/stefan/7774412/working/building/REAL300004087146 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/191 `/scratch/stefan/7774412/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CO1) `REAL300004087146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087146 none CNS(=O)(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.3', '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, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [51, 41, 11, 41, 41, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 51, 51, 51, 51, 11, 2, 2, 2, 2, 2, 2, 11] 77 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087146 none CNS(=O)(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.3', '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, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 6, 6, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 35, 35, 11, 11, 11, 1, 1, 17, 17, 17, 17, 1, 7, 21, 21, 11, 11, 11, 1] 77 rigid atoms, others: [2, 5, 6, 7, 8, 34, 21, 22, 27] set([0, 1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087146 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087146/1 /scratch/stefan/7774412/working/building/REAL300004087146 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/192 `/scratch/stefan/7774412/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N-]S(=O)(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CO1) `REAL300004087146.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087146/1/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: REAL300004087146 none C[N-]S(=O)(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [45, 31, 11, 31, 31, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 45, 45, 45, 11, 2, 2, 2, 2, 2, 2, 11] 73 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087146 none C[N-]S(=O)(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.2', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 5, 5, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 19, 35, 35, 11, 11, 11, 1, 1, 11, 11, 11, 1, 7, 19, 19, 11, 11, 11, 1] 73 rigid atoms, others: [33, 2, 5, 6, 7, 8, 21, 22, 26] set([0, 1, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087146 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087146 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087146/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087146/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087146 Building REAL300004087147 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087147' /scratch/stefan/7774412/working/building/REAL300004087147 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087147 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087147/0 /scratch/stefan/7774412/working/building/REAL300004087147 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/193 `/scratch/stefan/7774412/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C(C)O)S2)S1) `REAL300004087147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087147 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C(C)O)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 12, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 37, 42, 42, 20, 14, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 1, 20, 20, 20, 20, 37, 37, 14, 1, 12, 12, 12, 12, 36] 186 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087147 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C(C)O)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'O.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 12, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 20, 20, 20, 40, 40, 20, 1, 2, 2, 2, 2, 2, 2, 20, 40, 40, 40, 40, 120] 186 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087147 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087147 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087147/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087147 Building REAL300004087148 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087148' /scratch/stefan/7774412/working/building/REAL300004087148 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087148 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087148/0 /scratch/stefan/7774412/working/building/REAL300004087148 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/194 `/scratch/stefan/7774412/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087148 none COCC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [113, 83, 26, 26, 26, 26, 26, 26, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 113, 113, 113, 83, 83, 27, 27, 27, 26, 2, 2, 2, 2, 2, 2] 148 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 366 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087148 none COCC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 26, 26, 26, 53, 91, 91, 26, 26, 26, 30, 30, 30, 7, 7, 2, 2, 2, 1, 14, 52, 53, 27, 27, 27] 148 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087148 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087148 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087148/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087148 Building REAL300004087149 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087149' /scratch/stefan/7774412/working/building/REAL300004087149 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087149 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087149/0 /scratch/stefan/7774412/working/building/REAL300004087149 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/195 `/scratch/stefan/7774412/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN=C(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087149 none CCC1=NN=C(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 19, 19, 19, 19, 19, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2] 26 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087149 none CCC1=NN=C(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 11, 11, 11, 21, 24, 24, 11, 11, 11, 6, 6, 6, 6, 6, 2, 2, 2, 1, 11, 21, 21, 11, 11, 11] 26 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 30] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087149 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087149 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087149/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087149 Building REAL300004087150 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087150' /scratch/stefan/7774412/working/building/REAL300004087150 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087150 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087150/0 /scratch/stefan/7774412/working/building/REAL300004087150 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/196 `/scratch/stefan/7774412/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NC(C3=CC=CC=C3)=C2)S1) `REAL300004087150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087150 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NC(C3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 27, 27, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 13, 13, 13, 13, 25, 25, 9, 1, 5, 5, 1, 5, 5, 1] 49 rigid atoms, others: [37, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087150 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NC(C3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 35, 35, 22, 35, 35, 13, 1, 2, 2, 2, 2, 2, 2, 13, 35, 35, 19, 35, 35, 13] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087150 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NC(C3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 49, 49, 49, 35, 25, 20, 5, 20, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 35, 35, 35, 35, 49, 49, 25, 5, 1, 1, 1, 1, 1, 5] 49 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087150 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087150 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087150/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087150 Building REAL300004087151 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087151' /scratch/stefan/7774412/working/building/REAL300004087151 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087151 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087151/0 /scratch/stefan/7774412/working/building/REAL300004087151 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/197 `/scratch/stefan/7774412/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3F)C2)S1) `REAL300004087151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087151 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 43, 64, 64, 23, 14, 11, 1, 11, 1, 1, 1, 1, 1, 6, 6, 4, 6, 6, 6, 1, 23, 23, 23, 23, 43, 43, 14, 1, 1, 1, 1, 1, 6, 6, 4, 6, 1, 1] 153 rigid atoms, others: [32, 33, 34, 35, 40, 41, 10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 269 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087151 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 23, 23, 23, 23, 85, 85, 83, 85, 85, 85, 23, 1, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 85, 85, 85, 85, 23, 23] 153 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 171 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087151 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 15, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 153, 153, 153, 85, 52, 40, 6, 40, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 85, 85, 85, 85, 153, 153, 52, 6, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6] 153 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 605 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087151 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087151 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087151/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087151 Building REAL300004087152 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087152' /scratch/stefan/7774412/working/building/REAL300004087152 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087152 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087152/0 /scratch/stefan/7774412/working/building/REAL300004087152 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/198 `/scratch/stefan/7774412/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3Cl)C2)S1) `REAL300004087152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087152 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3Cl)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 39, 39, 39, 22, 14, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 2, 1, 22, 22, 22, 22, 39, 39, 14, 1, 1, 1, 1, 1, 2, 2, 1, 2, 1, 1] 39 rigid atoms, others: [32, 33, 34, 35, 40, 41, 10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39]) total number of confs: 158 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: REAL300004087152 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3Cl)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087152 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=CC=C3Cl)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 16, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 39, 39, 39, 22, 14, 11, 2, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 39, 39, 14, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2] 39 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41]) total number of confs: 153 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087152 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087152 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087152/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087152 Building REAL300004087153 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087153' /scratch/stefan/7774412/working/building/REAL300004087153 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087153 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087153/0 /scratch/stefan/7774412/working/building/REAL300004087153 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/199 `/scratch/stefan/7774412/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC(F)(F)F)C=N2)S1) `REAL300004087153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087153 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC(F)(F)F)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 15, 21, 21, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 16, 16, 16, 16, 1, 1, 8, 9, 9, 9, 15, 14, 5, 1, 1, 16, 16, 1] 58 rigid atoms, others: [32, 35, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 129 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087153 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC(F)(F)F)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 23, 33, 33, 33, 33, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 33, 33, 8] 58 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087153 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087153 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087153/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087153 Building REAL300004087154 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087154' /scratch/stefan/7774412/working/building/REAL300004087154 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087154 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087154/0 /scratch/stefan/7774412/working/building/REAL300004087154 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/200 `/scratch/stefan/7774412/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=C2)N=CN3C)S1) `REAL300004087154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087154 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=C2)N=CN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 21, 21, 21, 17, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 21, 21, 13, 1, 1, 1, 1, 2, 2, 2] 21 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 35, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087154 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=C2)N=CN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087154 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087154 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087154/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087154 Building REAL300004087155 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087155' /scratch/stefan/7774412/working/building/REAL300004087155 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087155 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087155/0 /scratch/stefan/7774412/working/building/REAL300004087155 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/201 `/scratch/stefan/7774412/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3OC=CC3=CC(F)=C2)S1) `REAL300004087155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087155 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3OC=CC3=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 8, 1, 1, 1, 1] 17 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087155 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3OC=CC3=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087155 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087155 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087155/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087155 Building REAL300004087156 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087156' /scratch/stefan/7774412/working/building/REAL300004087156 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087156 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087156/0 /scratch/stefan/7774412/working/building/REAL300004087156 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/202 `/scratch/stefan/7774412/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=CC=C3O2)S1) `REAL300004087156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087156 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=CC=C3O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 12, 21, 21, 21, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 20, 21, 9, 1, 2, 2, 2, 1, 1, 1] 21 rigid atoms, others: [33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087156 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=CC=C3O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 12, 11, 12, 12, 11, 11, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 11, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087156 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087156 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087156/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087156 Building REAL300004087157 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087157' /scratch/stefan/7774412/working/building/REAL300004087157 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087157 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087157/0 /scratch/stefan/7774412/working/building/REAL300004087157 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/203 `/scratch/stefan/7774412/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2NC(=O)NC2=O)S1) `REAL300004087157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087157 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2NC(=O)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 13, 13, 13, 11, 11, 11, 9, 11, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 9, 9, 6, 6, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087157 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2NC(=O)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 11, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 2, 2, 2, 5, 7, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 11, 11, 11] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087157 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087157 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087157/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087157 Building REAL300004087158 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087158' /scratch/stefan/7774412/working/building/REAL300004087158 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087158 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087158/0 /scratch/stefan/7774412/working/building/REAL300004087158 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/204 `/scratch/stefan/7774412/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(N(C)C)C=C2)S1) `REAL300004087158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087158 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 19, 19, 19, 17, 17, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 17, 17, 17, 17, 19, 19, 17, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 1, 1] 27 rigid atoms, others: [32, 33, 40, 41, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087158 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 11, 17, 17, 11, 15, 23, 23, 17, 17, 1, 2, 2, 2, 2, 2, 2, 11, 11, 17, 17, 23, 23, 23, 23, 23, 23, 17, 17] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087158 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087158 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087158/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087158 Building REAL300004087159 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087159' /scratch/stefan/7774412/working/building/REAL300004087159 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087159 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087159/0 /scratch/stefan/7774412/working/building/REAL300004087159 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/205 `/scratch/stefan/7774412/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(S(N)(=O)=O)=CC=C2C)S1) `REAL300004087159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087159 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(S(N)(=O)=O)=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 1, 5, 5, 1, 1, 2, 2, 2] 11 rigid atoms, others: [33, 34, 10, 12, 13, 14, 15, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 31, 32, 35, 36, 37]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087159 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(S(N)(=O)=O)=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 14, 8, 11, 11, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 9, 9, 9, 2, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 9, 9, 2, 3, 3, 3, 3] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087159 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087159 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087159/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087159 Building REAL300004087160 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087160' /scratch/stefan/7774412/working/building/REAL300004087160 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087160 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087160/0 /scratch/stefan/7774412/working/building/REAL300004087160 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/206 `/scratch/stefan/7774412/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C) `REAL300004087160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087160 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 14, 13, 13, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087160 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 13, 13, 14, 27, 27, 27, 13, 13, 13, 1, 1, 1, 1, 2, 2, 2, 1, 8, 26, 27, 14, 14, 14, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087160 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087160 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087160/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087160 Building REAL300004087161 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087161' /scratch/stefan/7774412/working/building/REAL300004087161 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087161 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087161/0 /scratch/stefan/7774412/working/building/REAL300004087161 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/207 `/scratch/stefan/7774412/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSCCS2)S1) `REAL300004087161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087161 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSCCS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 24, 24, 24, 19, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 24, 24, 13, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087161 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSCCS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 19] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 18] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087161 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087161/1 /scratch/stefan/7774412/working/building/REAL300004087161 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/208 `/scratch/stefan/7774412/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSCCS2)S1) `REAL300004087161.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087161/1/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: REAL300004087161 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSCCS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 5, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [155, 155, 155, 155, 201, 201, 201, 155, 55, 11, 1, 11, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23]) total number of confs: 488 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087161 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSCCS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 5, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 74, 74, 155, 155, 155, 155, 155, 1, 2, 2, 2, 2, 2, 155, 155, 155, 155, 155, 155, 155] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 18] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087161 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087161 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087161/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087161/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087161 Building REAL300004087162 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087162' /scratch/stefan/7774412/working/building/REAL300004087162 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087162 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087162/0 /scratch/stefan/7774412/working/building/REAL300004087162 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/209 `/scratch/stefan/7774412/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087162 none CC1=NNC(C)=C1CCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 8, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2] 13 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087162 none CC1=NNC(C)=C1CCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 8, 9, 10, 11, 11, 11, 15, 15, 15, 10, 10, 10, 2, 2, 2, 1, 2, 2, 2, 2, 2, 5, 5, 11, 15, 15, 11, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087162 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087162 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087162/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087162 Building REAL300004087163 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087163' /scratch/stefan/7774412/working/building/REAL300004087163 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087163 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087163/0 /scratch/stefan/7774412/working/building/REAL300004087163 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/210 `/scratch/stefan/7774412/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1) `REAL300004087163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087163 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 33, 35, 35, 19, 19, 19, 6, 19, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 19, 19, 19, 19, 33, 33, 19, 6, 6, 1, 10, 10, 10, 10] 41 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087163 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 10, 19, 19, 19, 19, 31, 31, 31, 31, 31, 19, 1, 2, 2, 2, 2, 2, 2, 10, 10, 19, 31, 31, 31, 31] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087163 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 41, 41, 41, 31, 31, 31, 18, 31, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 31, 41, 41, 31, 18, 18, 10, 1, 1, 1, 1] 41 rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 146 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087163 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087163/1 /scratch/stefan/7774412/working/building/REAL300004087163 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/211 `/scratch/stefan/7774412/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1) `REAL300004087163.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087163 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 191, 191, 191, 166, 101, 41, 8, 41, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 166, 166, 166, 166, 191, 191, 8, 8, 1, 8, 8, 8, 8] 195 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) 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: REAL300004087163 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 41, 41, 101, 166, 166, 166, 166, 179, 179, 179, 179, 179, 166, 1, 2, 2, 2, 3, 3, 101, 101, 166, 179, 179, 179, 179] 195 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087163 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 195, 195, 195, 179, 138, 83, 24, 83, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 179, 179, 179, 179, 195, 195, 24, 24, 8, 1, 1, 1, 1] 195 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 474 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087163 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087163 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087163/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087163/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087163 Building REAL300004087164 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087164' /scratch/stefan/7774412/working/building/REAL300004087164 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087164 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087164/0 /scratch/stefan/7774412/working/building/REAL300004087164 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/212 `/scratch/stefan/7774412/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN2C2=CC=C(F)C=C2)S1) `REAL300004087164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087164 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 31, 31, 16, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 2, 5, 5, 16, 16, 16, 16, 29, 29, 14, 1, 1, 5, 5, 5, 5] 33 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087164 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 4, 4, 16, 16, 16, 16, 16, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 2, 2, 2, 16, 16, 21, 21, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087164 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CN2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 33, 33, 33, 21, 19, 17, 5, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 19, 5, 5, 1, 1, 1, 1] 33 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087164 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087164 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087164/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087164 Building REAL300004087165 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087165' /scratch/stefan/7774412/working/building/REAL300004087165 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087165 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087165/0 /scratch/stefan/7774412/working/building/REAL300004087165 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/213 `/scratch/stefan/7774412/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=CC=N2)S1) `REAL300004087165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087165 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 31, 53, 53, 18, 13, 9, 1, 9, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 1, 18, 19, 19, 19, 31, 31, 13, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 82 rigid atoms, others: [40, 41, 10, 12, 13, 14, 15, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087165 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 56, 56, 56, 56, 56, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 56, 56, 56, 56, 56, 56, 56, 56, 18, 18] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087165 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCOCC3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 12, 5, 5, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 82, 82, 82, 56, 43, 41, 11, 41, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 10, 56, 56, 56, 56, 82, 82, 43, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 82 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 285 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087165 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087165 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087165/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087165 Building REAL300004087166 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087166' /scratch/stefan/7774412/working/building/REAL300004087166 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087166 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087166/0 /scratch/stefan/7774412/working/building/REAL300004087166 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/214 `/scratch/stefan/7774412/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087166 none CC1=NNC(C)=C1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 3, 3, 2, 2, 2] 9 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087166 none CC1=NNC(C)=C1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 11, 11, 11, 9, 9, 9, 2, 2, 2, 1, 2, 2, 2, 2, 2, 9, 11, 11, 9, 9, 9] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087166 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087166 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087166/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087166 Building REAL300004087167 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087167' /scratch/stefan/7774412/working/building/REAL300004087167 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087167 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087167/0 /scratch/stefan/7774412/working/building/REAL300004087167 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/215 `/scratch/stefan/7774412/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(S(N)(=O)=O)C=C2)S1) `REAL300004087167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087167 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(S(N)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 11, 17, 17, 8, 8, 8, 6, 8, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 8, 8, 8, 8, 11, 11, 8, 6, 6, 4, 4, 1, 1, 5, 5, 1, 1] 29 rigid atoms, others: [35, 36, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087167 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(S(N)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 8, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 6, 8, 8, 6, 8, 19, 19, 19, 8, 8, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 8, 8, 19, 19, 8, 8] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087167 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087167 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087167/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087167 Building REAL300004087168 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087168' /scratch/stefan/7774412/working/building/REAL300004087168 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087168 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087168/0 /scratch/stefan/7774412/working/building/REAL300004087168 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/216 `/scratch/stefan/7774412/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC2=CC=CC=C21) `REAL300004087168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087168 none COC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 10, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 11, 11, 11, 10, 10, 11, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11] 21 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087168 none COC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 21, 21, 21, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 11, 11, 11, 1, 1, 1, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 18, 19, 20, 21, 22, 23, 24, 36, 38, 37] set([32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087168 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087168 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087168/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087168 Building REAL300004087169 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087169' /scratch/stefan/7774412/working/building/REAL300004087169 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087169 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087169/0 /scratch/stefan/7774412/working/building/REAL300004087169 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/217 `/scratch/stefan/7774412/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NC=C2)S1) `REAL300004087169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087169 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 41, 46, 46, 22, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 2, 6, 6, 22, 23, 23, 23, 41, 41, 14, 1, 2, 2, 2, 6, 6, 6, 6] 54 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087169 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 22, 22, 22, 34, 34, 31, 34, 34, 1, 2, 2, 2, 2, 2, 2, 22, 23, 23, 23, 34, 34, 34, 34] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087169 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 54, 54, 54, 34, 26, 24, 6, 24, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 54, 54, 26, 6, 6, 6, 6, 1, 1, 1, 1] 54 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087169 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087169 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087169/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087169 Building REAL300004087170 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087170' /scratch/stefan/7774412/working/building/REAL300004087170 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087170 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087170/0 /scratch/stefan/7774412/working/building/REAL300004087170 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/218 `/scratch/stefan/7774412/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N2CCSCC2)S1) `REAL300004087170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087170 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N2CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 44, 46, 46, 23, 16, 15, 4, 15, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 23, 23, 23, 23, 44, 44, 16, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 49 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087170 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N2CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 18, 23, 23, 18, 23, 23, 18, 26, 26, 26, 26, 26, 1, 2, 2, 2, 2, 2, 2, 18, 23, 23, 18, 23, 23, 26, 26, 26, 26, 26, 26, 26, 26] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087170 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)N2CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 49, 49, 49, 26, 19, 17, 6, 17, 1, 6, 9, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 49, 49, 19, 6, 9, 9, 6, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 225 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087170 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087170/1 /scratch/stefan/7774412/working/building/REAL300004087170 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/219 `/scratch/stefan/7774412/working/3D/219' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)N2CCSCC2)S1) `REAL300004087170.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087170 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)N2CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 186, 189, 189, 146, 46, 8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 146, 146, 146, 146, 186, 186, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087170 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)N2CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 71, 71, 110, 146, 146, 110, 146, 146, 110, 159, 159, 159, 159, 159, 1, 2, 2, 2, 2, 2, 110, 146, 146, 110, 146, 146, 159, 159, 159, 159, 159, 159, 159, 159] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087170 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)N2CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 10, 5, 5, 14, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 199, 201, 201, 159, 59, 12, 6, 12, 1, 6, 8, 8, 6, 8, 8, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 199, 199, 6, 8, 8, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 44, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 495 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087170 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087170 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087170/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087170/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087170 Building REAL300004087171 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087171' /scratch/stefan/7774412/working/building/REAL300004087171 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087171 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087171/0 /scratch/stefan/7774412/working/building/REAL300004087171 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/220 `/scratch/stefan/7774412/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C(C)C)N2CC(C)OC(C)C2)S1) `REAL300004087171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087171 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C(C)C)N2CC(C)OC(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 14, 14, 8, 5, 5, 4, 5, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1] 14 rigid atoms, others: [50, 49, 39, 40, 41, 12, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087171 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C(C)C)N2CC(C)OC(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 65 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087171 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087171/1 /scratch/stefan/7774412/working/building/REAL300004087171 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/221 `/scratch/stefan/7774412/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C(C)C)N2CC(C)OC(C)C2)S1) `REAL300004087171.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087171/1/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: REAL300004087171 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C(C)C)N2CC(C)OC(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 54, 54, 54, 44, 17, 5, 4, 5, 1, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 54, 54, 4, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 1] 54 rigid atoms, others: [48, 49, 38, 39, 40, 44, 12, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 45, 46, 47]) total number of confs: 148 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087171 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C(C)C)N2CC(C)OC(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 41, 41, 41, 41, 41, 41, 44, 44, 44, 44, 44, 44, 44, 1, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087171 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087171 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087171/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087171/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087171 Building REAL300004087172 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087172' /scratch/stefan/7774412/working/building/REAL300004087172 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087172 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087172/0 /scratch/stefan/7774412/working/building/REAL300004087172 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/222 `/scratch/stefan/7774412/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2CCCCCC2)S1) `REAL300004087172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087172 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 27, 27, 27, 19, 15, 15, 5, 15, 1, 5, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 27, 27, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087172 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)N2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087172 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087172 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087172/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087172 Building REAL300004087173 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087173' /scratch/stefan/7774412/working/building/REAL300004087173 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087173 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087173/0 /scratch/stefan/7774412/working/building/REAL300004087173 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/223 `/scratch/stefan/7774412/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(NC3=CC=CC=N3)=N2)S1) `REAL300004087173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087173 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(NC3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 15, 31, 31, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 13, 38, 38, 38, 38, 38, 1, 9, 9, 9, 9, 15, 15, 6, 1, 13, 38, 38, 38, 38] 120 rigid atoms, others: [10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087173 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(NC3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 45, 80, 80, 80, 80, 80, 9, 1, 2, 2, 2, 2, 2, 2, 9, 45, 80, 80, 80, 80] 120 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087173 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(NC3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 8, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 120, 120, 120, 80, 56, 56, 38, 56, 38, 38, 38, 11, 1, 1, 1, 1, 1, 1, 1, 38, 80, 80, 80, 80, 120, 120, 56, 38, 11, 1, 1, 1, 1] 120 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 402 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087173 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087173 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087173/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087173 Building REAL300004087174 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087174' /scratch/stefan/7774412/working/building/REAL300004087174 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087174 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087174/0 /scratch/stefan/7774412/working/building/REAL300004087174 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/224 `/scratch/stefan/7774412/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087174 none CCC(CC)N1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 7, 19, 28, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 28, 28, 28, 28, 28, 19, 28, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2] 43 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087174 none CCC(CC)N1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 1, 7, 10, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 13, 21, 21, 7, 6, 7, 1, 10, 10, 10, 10, 10, 7, 10, 10, 10, 10, 10, 1, 1, 4, 13, 13, 7, 7, 7] 43 rigid atoms, others: [34, 35, 5, 6, 7, 8, 9, 2, 22] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087174 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087174 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087174/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087174 Building REAL300004087175 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087175' /scratch/stefan/7774412/working/building/REAL300004087175 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087175 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087175/0 /scratch/stefan/7774412/working/building/REAL300004087175 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/225 `/scratch/stefan/7774412/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(=O)C3=CC=CC=C32)S1) `REAL300004087175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087175 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(=O)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 21, 21, 21, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 79 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: REAL300004087175 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(=O)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087175 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087175/1 /scratch/stefan/7774412/working/building/REAL300004087175 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/226 `/scratch/stefan/7774412/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC(=O)C3=CC=CC=C32)S1) `REAL300004087175.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087175/1/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: REAL300004087175 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC(=O)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 130, 130, 130, 93, 26, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 130, 130, 1, 1, 1, 1, 1, 1, 1, 1, 1] 130 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087175 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC(=O)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 63, 63, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 1, 2, 2, 2, 2, 2, 93, 93, 93, 93, 93, 93, 93, 93, 93] 130 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087175 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087175 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087175/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087175/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087175 Building REAL300004087176 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087176' /scratch/stefan/7774412/working/building/REAL300004087176 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087176 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087176/0 /scratch/stefan/7774412/working/building/REAL300004087176 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/227 `/scratch/stefan/7774412/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2N)S1) `REAL300004087176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087176 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 7, 1, 2, 2, 2, 2, 2] 21 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087176 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C)N=C2N)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 3, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087176 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087176 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087176/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087176 Building REAL300004087177 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087177' /scratch/stefan/7774412/working/building/REAL300004087177 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087177 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087177/0 /scratch/stefan/7774412/working/building/REAL300004087177 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/228 `/scratch/stefan/7774412/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=CC=C(O)C(F)=C2)S1) `REAL300004087177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087177 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=CC=C(O)C(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 47, 47, 47, 35, 35, 35, 20, 35, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 47, 47, 35, 19, 19, 14, 14, 7, 7, 1, 1, 2, 1] 94 rigid atoms, others: [36, 37, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087177 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC2=CC=C(O)C(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 12, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 12, 19, 35, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 2, 2, 2, 8, 8, 12, 12, 19, 19, 35, 35, 70, 35] 94 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087177 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087177 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087177/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087177 Building REAL300004087178 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087178' /scratch/stefan/7774412/working/building/REAL300004087178 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087178 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087178/0 /scratch/stefan/7774412/working/building/REAL300004087178 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/229 `/scratch/stefan/7774412/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087178 none COC1=CN=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 8, 9, 9, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 10, 10, 10, 8, 9, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087178 none COC1=CN=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 17, 17, 17, 9, 9, 8, 1, 2, 2, 2, 1, 1, 8, 17, 17, 9, 9, 9] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 24, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087178 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087178 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087178/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087178 Building REAL300004087179 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087179' /scratch/stefan/7774412/working/building/REAL300004087179 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087179 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087179/0 /scratch/stefan/7774412/working/building/REAL300004087179 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/230 `/scratch/stefan/7774412/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087179 none CCC1=CC=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [27, 13, 13, 12, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 27, 27, 27, 27, 27, 12, 13, 2, 2, 2, 2, 1, 1, 13] 41 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087179 none CCC1=CC=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 21, 25, 25, 13, 12, 13, 1, 7, 7, 7, 7, 7, 1, 1, 10, 21, 21, 13, 13, 13, 1] 41 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 20, 26, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087179 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087179 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087179/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087179 Building REAL300004087180 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087180' /scratch/stefan/7774412/working/building/REAL300004087180 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087180 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087180/0 /scratch/stefan/7774412/working/building/REAL300004087180 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/231 `/scratch/stefan/7774412/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=CC1=CC=CC=C1)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087180 none COC(=CC1=CC=CC=C1)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 3, 18, 18, 27, 27, 18, 27, 27, 2, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 26, 26, 26, 18, 27, 27, 18, 27, 27, 2, 2, 2, 2, 2, 2] 42 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 126 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087180 none COC(=CC1=CC=CC=C1)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20, 20, 27, 27, 27, 42, 42, 42, 27, 27, 27, 16, 16, 16, 5, 1, 1, 1, 1, 1, 20, 42, 42, 27, 27, 27] 42 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087180 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087180/1 /scratch/stefan/7774412/working/building/REAL300004087180 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/232 `/scratch/stefan/7774412/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=CC1=CC=CC=C1)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087180.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087180/1/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: REAL300004087180 none COC(=CC1=CC=CC=C1)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 142, 59, 142, 142, 176, 176, 142, 176, 176, 13, 59, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 148, 148, 148, 142, 176, 176, 172, 176, 176, 2, 2, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 662 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087180 none COC(=CC1=CC=CC=C1)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 33, 33, 103, 176, 176, 176, 200, 201, 201, 176, 176, 176, 18, 18, 18, 4, 1, 1, 1, 1, 1, 200, 200, 176, 176, 176] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087180 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087180 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087180/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087180/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087180 Building REAL300004087181 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087181' /scratch/stefan/7774412/working/building/REAL300004087181 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087181 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087181/0 /scratch/stefan/7774412/working/building/REAL300004087181 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/233 `/scratch/stefan/7774412/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=NNN=C32)S1) `REAL300004087181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087181 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=NNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 8, 1, 1, 1, 1] 15 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087181 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=NNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'N.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087181 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087181 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087181/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087181 Building REAL300004087182 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087182' /scratch/stefan/7774412/working/building/REAL300004087182 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087182 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087182/0 /scratch/stefan/7774412/working/building/REAL300004087182 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/234 `/scratch/stefan/7774412/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2CCCC3)S1) `REAL300004087182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087182 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 16, 16, 16, 9, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087182 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087182 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087182 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087182/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087182 Building REAL300004087183 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087183' /scratch/stefan/7774412/working/building/REAL300004087183 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087183 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087183/0 /scratch/stefan/7774412/working/building/REAL300004087183 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/235 `/scratch/stefan/7774412/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=C(C)N(C)N=C2)S1) `REAL300004087183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087183 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 37, 37, 37, 23, 23, 23, 7, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 37, 37, 23, 8, 7, 2, 2, 2, 2, 2, 2, 1] 37 rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087183 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 2, 2, 2, 9, 9, 23, 23, 23, 23, 23, 23, 23] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087183 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087183 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087183/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087183 Building REAL300004087184 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087184' /scratch/stefan/7774412/working/building/REAL300004087184 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087184 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087184/0 /scratch/stefan/7774412/working/building/REAL300004087184 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/236 `/scratch/stefan/7774412/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=CN=C3C=C2)S1) `REAL300004087184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087184 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 2, 2, 2, 1, 1, 1, 1] 25 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087184 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087184 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087184 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087184/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087184 Building REAL300004087185 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087185' /scratch/stefan/7774412/working/building/REAL300004087185 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087185 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087185/0 /scratch/stefan/7774412/working/building/REAL300004087185 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/237 `/scratch/stefan/7774412/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN3N=NN=C23)S1) `REAL300004087185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087185 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN3N=NN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 1, 1, 1] 7 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087185 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN3N=NN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 3, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 3] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087185 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087185 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087185/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087185 Building REAL300004087186 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087186' /scratch/stefan/7774412/working/building/REAL300004087186 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087186 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087186/0 /scratch/stefan/7774412/working/building/REAL300004087186 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/238 `/scratch/stefan/7774412/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C(C)C)S1) `REAL300004087186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087186 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 39, 46, 46, 21, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 21, 21, 21, 21, 39, 39, 14, 1, 1, 6, 6, 6, 6, 6, 6, 6] 49 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087186 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 21, 21, 21, 21, 21, 27, 27, 1, 2, 2, 2, 2, 2, 2, 21, 21, 27, 27, 27, 27, 27, 27, 27] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087186 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087186 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087186/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087186 Building REAL300004087187 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087187' /scratch/stefan/7774412/working/building/REAL300004087187 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087187 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087187/0 /scratch/stefan/7774412/working/building/REAL300004087187 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/239 `/scratch/stefan/7774412/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2CC2)S1) `REAL300004087187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087187 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 48, 64, 64, 24, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 25, 25, 25, 48, 48, 14, 1, 2, 2, 2, 8, 8, 8, 8, 8] 80 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 289 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087187 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 24, 24, 24, 24, 46, 46, 1, 2, 2, 2, 2, 2, 2, 24, 25, 25, 25, 46, 46, 46, 46, 46] 80 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087187 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 80, 80, 80, 46, 33, 30, 8, 30, 8, 8, 8, 8, 8, 1, 1, 1, 1, 46, 46, 46, 46, 80, 80, 33, 8, 8, 8, 8, 1, 1, 1, 1, 1] 80 rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087187 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087187 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087187/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087187 Building REAL300004087188 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087188' /scratch/stefan/7774412/working/building/REAL300004087188 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087188 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087188/0 /scratch/stefan/7774412/working/building/REAL300004087188 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/240 `/scratch/stefan/7774412/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=C(C)N(C)N=C2)S1) `REAL300004087188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087188 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 31, 31, 31, 20, 20, 18, 12, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 31, 31, 20, 12, 12, 8, 8, 2, 2, 2, 2, 2, 2, 1] 31 rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 151 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087188 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 5, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 10, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 8, 8, 10, 10, 20, 20, 20, 20, 20, 20, 20] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087188 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087188 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087188/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087188 Building REAL300004087189 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087189' /scratch/stefan/7774412/working/building/REAL300004087189 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087189 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087189/0 /scratch/stefan/7774412/working/building/REAL300004087189 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/241 `/scratch/stefan/7774412/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087189 none COC1=NOC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 12, 12, 12, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 18, 18, 18, 4, 4, 2, 2, 2, 3, 3, 2, 2, 2, 12] 29 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087189 none COC1=NOC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 11, 11, 12, 12, 12, 12, 12, 21, 25, 25, 12, 12, 12, 1, 3, 3, 3, 7, 7, 12, 12, 12, 21, 21, 12, 12, 12, 1] 29 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 21] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087189 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087189 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087189/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087189 Building REAL300004087190 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087190' /scratch/stefan/7774412/working/building/REAL300004087190 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087190 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087190/0 /scratch/stefan/7774412/working/building/REAL300004087190 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/242 `/scratch/stefan/7774412/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2NN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C2=CC=C1) `REAL300004087190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087190 none COC1=C2NN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [27, 16, 16, 16, 16, 16, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 16, 17, 17, 17, 27, 27, 27, 16, 2, 2, 2, 2, 2, 2, 17, 17, 17] 37 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087190 none COC1=C2NN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 16, 16, 17, 29, 37, 37, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 1, 11, 29, 29, 17, 17, 17, 1, 1, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 34, 35, 20, 21, 22, 23, 36, 27] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087190 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087190/1 /scratch/stefan/7774412/working/building/REAL300004087190 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/243 `/scratch/stefan/7774412/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NN=C21) `REAL300004087190.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087190/1/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: REAL300004087190 none COC1=CC=CC2=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NN=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [47, 25, 25, 25, 25, 25, 25, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 25, 25, 25, 47, 47, 47, 25, 25, 25, 2, 2, 2, 2, 2, 2, 25] 59 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087190 none COC1=CC=CC2=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NN=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 15, 25, 25, 25, 48, 59, 59, 25, 25, 25, 1, 1, 1, 4, 4, 4, 1, 1, 1, 15, 48, 48, 26, 26, 26, 1] 59 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 36, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087190 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087190 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087190/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087190/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087190 Building REAL300004087191 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087191' /scratch/stefan/7774412/working/building/REAL300004087191 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087191 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087191/0 /scratch/stefan/7774412/working/building/REAL300004087191 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/244 `/scratch/stefan/7774412/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C)C(O)=C2)S1) `REAL300004087191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087191 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C)C(O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 73, 73, 73, 37, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 73, 73, 21, 6, 6, 1, 1, 2, 2, 2, 2, 1] 146 rigid atoms, others: [36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 317 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087191 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C)C(O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 5, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 9, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 3, 3, 2, 9, 9, 37, 37, 37, 37, 37, 74, 37] 146 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 165 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087191 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087191 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087191/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087191 Building REAL300004087192 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087192' /scratch/stefan/7774412/working/building/REAL300004087192 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087192 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087192/0 /scratch/stefan/7774412/working/building/REAL300004087192 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/245 `/scratch/stefan/7774412/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CN2C)S1) `REAL300004087192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087192 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 17, 17, 17, 13, 13, 13, 9, 13, 9, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 13, 9, 9, 1, 1, 2, 2, 2] 17 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087192 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087192 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087192 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087192/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087192 Building REAL300004087193 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087193' /scratch/stefan/7774412/working/building/REAL300004087193 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087193 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087193/0 /scratch/stefan/7774412/working/building/REAL300004087193 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/246 `/scratch/stefan/7774412/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CS2)S1) `REAL300004087193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087193 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 41, 41, 41, 36, 36, 32, 13, 31, 13, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 41, 41, 36, 13, 13, 1, 1] 41 rigid atoms, others: [13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087193 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 13, 13, 36, 36, 36, 36, 1, 2, 2, 2, 2, 2, 2, 13, 13, 36, 36] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087193 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087193 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087193/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087193 Building REAL300004087194 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087194' /scratch/stefan/7774412/working/building/REAL300004087194 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087194 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087194/0 /scratch/stefan/7774412/working/building/REAL300004087194 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/247 `/scratch/stefan/7774412/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC3=NC=NC3=C2)S1) `REAL300004087194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087194 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC3=NC=NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087194 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC3=NC=NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087194 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087194/1 /scratch/stefan/7774412/working/building/REAL300004087194 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/248 `/scratch/stefan/7774412/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3NC=NC3=C2)S1) `REAL300004087194.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087194/1/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: REAL300004087194 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3NC=NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087194 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3NC=NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087194 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087194 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087194/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087194/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087194 Building REAL300004087195 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087195' /scratch/stefan/7774412/working/building/REAL300004087195 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087195 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087195/0 /scratch/stefan/7774412/working/building/REAL300004087195 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/249 `/scratch/stefan/7774412/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC3=NC=CN=C3C=C2)S1) `REAL300004087195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087195 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC3=NC=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 12, 13, 13, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 12, 12, 5, 1, 1, 1, 1] 13 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087195 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC3=NC=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 8, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087195 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087195 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087195/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087195 Building REAL300004087196 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087196' /scratch/stefan/7774412/working/building/REAL300004087196 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087196 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087196/0 /scratch/stefan/7774412/working/building/REAL300004087196 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/250 `/scratch/stefan/7774412/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC(CC2CC2)=N1) `REAL300004087196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087196 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 72, 109, 109, 20, 21, 21, 21, 2, 2, 2, 2, 2, 2, 72, 72, 109, 109, 109, 109, 109] 169 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087196 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 11, 20, 20, 20, 40, 83, 83, 20, 20, 20, 1, 1, 1, 7, 23, 23, 1, 2, 2, 2, 11, 40, 40, 21, 21, 21, 7, 7, 23, 23, 23, 23, 23] 169 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 384 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087196 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC(CC2CC2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 75, 75, 83, 109, 109, 109, 169, 169, 169, 109, 109, 109, 23, 5, 1, 1, 1, 1, 23, 23, 23, 23, 83, 169, 169, 109, 109, 109, 5, 5, 1, 1, 1, 1, 1] 169 rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 622 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087196 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087196 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087196/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087196 Building REAL300004087197 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087197' /scratch/stefan/7774412/working/building/REAL300004087197 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087197 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087197/0 /scratch/stefan/7774412/working/building/REAL300004087197 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/251 `/scratch/stefan/7774412/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCN(CC(F)F)CC2)S1) `REAL300004087197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087197 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCN(CC(F)F)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 14, 24, 24, 10, 10, 10, 5, 10, 1, 1, 1, 1, 1, 1, 7, 11, 11, 1, 1, 10, 10, 10, 10, 14, 14, 10, 5, 5, 1, 1, 1, 1, 1, 7, 7, 11, 1, 1, 1, 1] 41 rigid atoms, others: [32, 33, 34, 35, 36, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087197 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCN(CC(F)F)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 23, 30, 30, 10, 10, 1, 2, 2, 2, 3, 3, 2, 6, 6, 10, 10, 10, 10, 10, 23, 23, 30, 10, 10, 10, 10] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 154 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087197 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087197 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087197/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087197 Building REAL300004087198 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087198' /scratch/stefan/7774412/working/building/REAL300004087198 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087198 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087198/0 /scratch/stefan/7774412/working/building/REAL300004087198 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/252 `/scratch/stefan/7774412/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=N3)=NO2)S1) `REAL300004087198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087198 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=N3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 19, 35, 35, 35, 18, 14, 12, 1, 12, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 18, 19, 19, 19, 35, 35, 14, 1, 4, 4, 3, 3] 35 rigid atoms, others: [10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087198 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=N3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 19, 19, 19, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 19, 19, 19, 18] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087198 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CC=N3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 35, 35, 35, 19, 15, 14, 3, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 19, 35, 35, 14, 4, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 140 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087198 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087198 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087198/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087198 Building REAL300004087199 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087199' /scratch/stefan/7774412/working/building/REAL300004087199 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087199 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087199/0 /scratch/stefan/7774412/working/building/REAL300004087199 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/253 `/scratch/stefan/7774412/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1) `REAL300004087199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087199 none CCNC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [54, 40, 22, 22, 22, 22, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 22, 54, 54, 54, 54, 54, 40, 22, 2, 2, 2, 2, 2, 2] 89 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087199 none CCNC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 1, 12, 12, 14, 22, 22, 22, 40, 61, 61, 22, 22, 22, 1, 21, 21, 21, 21, 21, 7, 1, 14, 40, 40, 23, 23, 23] 89 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 313 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087199 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087199 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087199/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087199 Building REAL300004087200 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087200' /scratch/stefan/7774412/working/building/REAL300004087200 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087200 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087200/0 /scratch/stefan/7774412/working/building/REAL300004087200 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/254 `/scratch/stefan/7774412/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N=C1) `REAL300004087200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087200 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [22, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 14, 14, 13, 13, 13, 13, 22, 22, 22, 2, 2, 2, 2, 2, 2, 13, 14, 14, 13, 13] 31 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087200 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 9, 9, 11, 13, 14, 14, 27, 31, 31, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 27, 27, 14, 14, 14, 1, 1, 1, 1, 1] 31 rigid atoms, others: [1, 2, 3, 4, 37, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24, 36, 38] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087200 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087200 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087200/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087200 Building REAL300004087201 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087201' /scratch/stefan/7774412/working/building/REAL300004087201 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087201 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087201/0 /scratch/stefan/7774412/working/building/REAL300004087201 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/255 `/scratch/stefan/7774412/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCC3)CCCCC2)S1) `REAL300004087201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087201 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCC3)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 1, 3, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [51, 44, 10, 43, 12, 13, 46, 45, 48, 49, 50, 19, 20, 21, 22, 23, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087201 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCC3)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 5, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 49 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087201 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCC3)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 67 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087201 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087201/1 /scratch/stefan/7774412/working/building/REAL300004087201 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/256 `/scratch/stefan/7774412/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCC3)CCCCC2)S1) `REAL300004087201.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087201 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCC3)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 113, 164, 174, 174, 113, 19, 5, 1, 5, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 113, 113, 113, 113, 164, 164, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 41, 10, 43, 12, 13, 46, 44, 48, 49, 50, 19, 20, 21, 22, 23, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 501 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087201 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCC3)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 63, 63, 113, 147, 147, 147, 147, 147, 113, 113, 113, 113, 113, 1, 2, 2, 2, 2, 2, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 113, 113, 113, 113, 113, 113, 113, 113, 113, 113] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087201 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCC3)CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 201, 201, 201, 147, 43, 13, 9, 13, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 147, 147, 147, 147, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 526 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087201 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087201 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087201/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087201/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087201 Building REAL300004087202 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087202' /scratch/stefan/7774412/working/building/REAL300004087202 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087202 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087202/0 /scratch/stefan/7774412/working/building/REAL300004087202 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/257 `/scratch/stefan/7774412/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CNC3=CC=CC(Cl)=C23)S1) `REAL300004087202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087202 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CNC3=CC=CC(Cl)=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 55, 55, 55, 33, 33, 31, 6, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 55, 55, 33, 6, 6, 1, 1, 1, 1, 1] 55 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087202 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CNC3=CC=CC(Cl)=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 15, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 2, 2, 2, 15, 15, 33, 33, 33, 33, 33] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087202 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087202 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087202/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087202 Building REAL300004087203 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087203' /scratch/stefan/7774412/working/building/REAL300004087203 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087203 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087203/0 /scratch/stefan/7774412/working/building/REAL300004087203 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/258 `/scratch/stefan/7774412/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C(C)=CC(C)=NC2=O)S1) `REAL300004087203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087203 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C(C)=CC(C)=NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 5, 1, 1, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 7, 7, 7, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 3, 3, 2, 2, 2, 1, 2, 2, 2] 7 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087203 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C(C)=CC(C)=NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 5, 1, 1, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 3, 3, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087203 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087203/1 /scratch/stefan/7774412/working/building/REAL300004087203 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/259 `/scratch/stefan/7774412/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C(C)=CC(C)=NC2=O)S1) `REAL300004087203.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087203/1/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: REAL300004087203 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C(C)=CC(C)=NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 5, 1, 1, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 201, 201, 201, 179, 55, 17, 3, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 201, 201, 3, 3, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 400 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087203 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C(C)=CC(C)=NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 5, 1, 1, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 74, 74, 166, 179, 179, 179, 179, 179, 179, 179, 179, 1, 2, 2, 2, 2, 2, 166, 166, 179, 179, 179, 179, 179, 179, 179] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087203 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087203 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087203/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087203/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087203 Building REAL300004087204 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087204' /scratch/stefan/7774412/working/building/REAL300004087204 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087204 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087204/0 /scratch/stefan/7774412/working/building/REAL300004087204 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/260 `/scratch/stefan/7774412/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087204 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 59, 59, 59, 36, 26, 24, 7, 24, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 36, 36, 36, 36, 59, 59, 26, 7, 7, 7, 7, 1, 1, 1, 1] 59 rigid atoms, others: [35, 36, 37, 38, 12, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087204 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 36, 36, 27, 31, 36, 36, 36, 36, 36, 1, 2, 2, 2, 2, 2, 2, 24, 25, 25, 25, 36, 36, 36, 36] 59 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087204 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087204/1 /scratch/stefan/7774412/working/building/REAL300004087204 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/261 `/scratch/stefan/7774412/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087204.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087204/1/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: REAL300004087204 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 70, 21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 163, 163, 163, 163, 201, 201, 7, 7, 7, 7, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087204 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 53, 53, 132, 132, 163, 163, 136, 145, 163, 163, 163, 163, 163, 1, 2, 2, 2, 2, 2, 132, 132, 132, 132, 163, 163, 163, 163] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087204 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087204 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087204/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087204/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087204 Building REAL300004087205 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087205' /scratch/stefan/7774412/working/building/REAL300004087205 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087205 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087205/0 /scratch/stefan/7774412/working/building/REAL300004087205 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/262 `/scratch/stefan/7774412/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1NC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087205 none COC1=CC=CC=C1NC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 25, 25, 25, 13, 25, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 15, 17, 17, 17, 32, 53, 53, 17, 17, 17, 47, 47, 47, 25, 25, 25, 25, 10, 1, 1, 1, 1, 15, 32, 32, 17, 17, 17] 201 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 339 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087205 none COC1=CC=CC=C1NC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 25, 25, 109, 109, 119, 121, 121, 121, 194, 201, 201, 121, 121, 121, 3, 3, 3, 1, 1, 1, 1, 10, 25, 25, 25, 25, 119, 194, 194, 121, 121, 121] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 768 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087205 none COC1=CC=CC=C1NC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 121, 121, 121, 98, 121, 121, 77, 17, 17, 17, 16, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 135, 135, 135, 121, 121, 121, 121, 77, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [17, 18, 19, 20, 21, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 429 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087205 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087205 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087205/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087205 Building REAL300004087206 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087206' /scratch/stefan/7774412/working/building/REAL300004087206 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087206 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087206/0 /scratch/stefan/7774412/working/building/REAL300004087206 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/263 `/scratch/stefan/7774412/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(Cl)=C1) `REAL300004087206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087206 none CCCCOC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [68, 56, 27, 13, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 68, 68, 68, 68, 68, 56, 56, 27, 27, 3, 3, 2, 2, 2, 2, 2, 2, 3] 96 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 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: 333 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087206 none CCCCOC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [45, 37, 16, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 13, 13, 3, 3, 3, 1, 1, 1, 46, 46, 46, 45, 45, 37, 37, 16, 16, 1, 1, 3, 5, 5, 3, 3, 3, 1] 96 rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 42, 22, 23, 24] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087206 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087206 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087206/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087206 Building REAL300004087207 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087207' /scratch/stefan/7774412/working/building/REAL300004087207 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087207 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087207/0 /scratch/stefan/7774412/working/building/REAL300004087207 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/264 `/scratch/stefan/7774412/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(Br)C(O)=C2)S1) `REAL300004087207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087207 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(Br)C(O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 79, 79, 79, 41, 23, 21, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 79, 79, 23, 7, 7, 1, 1, 2, 1] 158 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087207 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(Br)C(O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 17, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 11, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 3, 3, 2, 11, 11, 41, 41, 82, 41] 158 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087207 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087207 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087207/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087207 Building REAL300004087208 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087208' /scratch/stefan/7774412/working/building/REAL300004087208 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087208 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087208/0 /scratch/stefan/7774412/working/building/REAL300004087208 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/265 `/scratch/stefan/7774412/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSC(C3=CC=CC=C3O)=N2)S1) `REAL300004087208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087208 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSC(C3=CC=CC=C3O)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 248 conformations in input total number of sets (complete confs): 248 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 33, 44, 44, 17, 12, 10, 1, 10, 1, 1, 1, 1, 1, 12, 12, 1, 12, 12, 12, 1, 17, 17, 17, 17, 33, 33, 12, 1, 1, 1, 12, 12, 12, 12, 25] 248 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087208 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSC(C3=CC=CC=C3O)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 248 conformations in input total number of sets (complete confs): 248 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 17, 17, 17, 17, 84, 84, 62, 84, 84, 84, 17, 1, 2, 2, 2, 2, 2, 3, 17, 17, 17, 84, 84, 84, 84, 168] 248 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 394 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087208 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CSC(C3=CC=CC=C3O)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 248 conformations in input total number of sets (complete confs): 248 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 124, 124, 124, 84, 66, 62, 12, 62, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 84, 84, 84, 84, 124, 124, 66, 12, 12, 12, 1, 1, 1, 1, 2] 248 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 431 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087208 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087208/1 /scratch/stefan/7774412/working/building/REAL300004087208 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/266 `/scratch/stefan/7774412/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSC(C3=CC=CC=C3O)=N2)S1) `REAL300004087208.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087208 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSC(C3=CC=CC=C3O)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [68, 68, 68, 68, 97, 114, 114, 68, 21, 6, 1, 6, 1, 1, 1, 1, 1, 12, 12, 2, 12, 12, 12, 1, 68, 68, 68, 68, 97, 97, 1, 1, 1, 12, 12, 12, 12, 25] 402 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087208 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSC(C3=CC=CC=C3O)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 39, 39, 68, 68, 68, 68, 171, 171, 145, 171, 171, 171, 68, 1, 2, 2, 2, 2, 2, 68, 68, 68, 171, 171, 171, 171, 342] 402 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087208 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CSC(C3=CC=CC=C3O)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [171, 171, 171, 171, 201, 201, 201, 171, 92, 38, 12, 38, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 171, 171, 171, 171, 201, 201, 12, 12, 12, 1, 1, 1, 1, 2] 402 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37]) total number of confs: 472 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087208 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087208 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087208/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087208/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087208 Building REAL300004087209 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087209' /scratch/stefan/7774412/working/building/REAL300004087209 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087209 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087209/0 /scratch/stefan/7774412/working/building/REAL300004087209 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/267 `/scratch/stefan/7774412/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCO1) `REAL300004087209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087209 none CCCC1CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [54, 51, 19, 19, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 19, 19, 19, 54, 54, 54, 54, 54, 51, 51, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19] 93 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) 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: REAL300004087209 none CCCC1CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [11, 9, 1, 1, 1, 1, 1, 13, 13, 15, 19, 19, 19, 36, 54, 54, 19, 18, 19, 1, 1, 1, 11, 11, 11, 11, 11, 9, 9, 1, 1, 1, 1, 15, 36, 36, 19, 19, 19, 1, 1, 1, 1] 93 rigid atoms, others: [32, 2, 3, 4, 5, 6, 39, 40, 41, 42, 19, 20, 21, 29, 30, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087209 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087209 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087209/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087209 Building REAL300004087210 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087210' /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004087210 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087210/0 /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/268 `/scratch/stefan/7774412/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(CN(C)CC4)C3=C2)S1) `REAL300004087210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087210 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(CN(C)CC4)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 10, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 38, 40, 32, 39, 26, 27, 28, 29, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087210 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(CN(C)CC4)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 10, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087210/1 /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/269 `/scratch/stefan/7774412/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(C[N@H+](C)CC4)C3=C2)S1) `REAL300004087210.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087210/1/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: REAL300004087210 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(C[N@H+](C)CC4)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 9, 6, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1] 3 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 40, 32, 41, 39, 33, 27, 28, 29, 30, 31]) total number of confs: 13 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087210 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(C[N@H+](C)CC4)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 9, 6, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087210/2 /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/270 `/scratch/stefan/7774412/working/3D/270' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(C[N@@H+](C)CC4)C3=C2)S1) `REAL300004087210.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087210/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087210 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(C[N@@H+](C)CC4)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 9, 6, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1] 3 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 40, 32, 41, 39, 33, 27, 28, 29, 30, 31]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087210 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3NC4=C(C[N@@H+](C)CC4)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 5, 9, 6, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087210 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087210 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087210/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087210/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087210/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087210 Building REAL300004087211 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087211' /scratch/stefan/7774412/working/building/REAL300004087211 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087211 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087211/0 /scratch/stefan/7774412/working/building/REAL300004087211 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/271 `/scratch/stefan/7774412/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2NC2CCCCC2)S1) `REAL300004087211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087211 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2NC2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 41, 58, 58, 22, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 22, 22, 22, 22, 41, 41, 14, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 140 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 269 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087211 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2NC2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 22, 22, 22, 49, 86, 86, 86, 86, 86, 1, 2, 2, 2, 2, 2, 2, 22, 22, 22, 22, 49, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86] 140 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 275 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087211 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2NC2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 140, 140, 140, 86, 70, 64, 18, 64, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 140, 140, 70, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 140 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 531 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087211 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087211 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087211/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087211 Building REAL300004087212 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087212' /scratch/stefan/7774412/working/building/REAL300004087212 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087212 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087212/0 /scratch/stefan/7774412/working/building/REAL300004087212 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/272 `/scratch/stefan/7774412/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3C=C(Cl)C=C(Cl)C3=N2)S1) `REAL300004087212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087212 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3C=C(Cl)C=C(Cl)C3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 1, 16, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 10, 17, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 17, 17, 8, 1, 1, 1] 17 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087212 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3C=C(Cl)C=C(Cl)C3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 1, 16, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 10, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087212 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087212 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087212/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087212 Building REAL300004087213 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087213' /scratch/stefan/7774412/working/building/REAL300004087213 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087213 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087213/0 /scratch/stefan/7774412/working/building/REAL300004087213 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/273 `/scratch/stefan/7774412/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087213 none COC1=C(Br)C=CC(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 6, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 9, 9, 9, 6, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087213 none COC1=C(Br)C=CC(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 13, 13, 13, 7, 7, 6, 3, 3, 3, 1, 1, 2, 2, 2, 7, 13, 13, 7, 7, 7] 17 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087213 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087213 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087213/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087213 Building REAL300004087214 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087214' /scratch/stefan/7774412/working/building/REAL300004087214 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087214 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087214/0 /scratch/stefan/7774412/working/building/REAL300004087214 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/274 `/scratch/stefan/7774412/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3C=NC4=CC=CC=C43)N=C2)S1) `REAL300004087214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087214 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3C=NC4=CC=CC=C43)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 19, 19, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 17, 17, 7, 1, 1, 6, 6, 6, 6, 6, 1] 29 rigid atoms, others: [34, 35, 41, 10, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087214 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3C=NC4=CC=CC=C43)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 20, 20, 20, 20, 20, 9] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087214 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3C=NC4=CC=CC=C43)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 29, 29, 29, 20, 18, 18, 6, 18, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 29, 29, 18, 6, 6, 1, 1, 1, 1, 1, 6] 29 rigid atoms, others: [36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41]) total number of confs: 95 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087214 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087214 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087214/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087214 Building REAL300004087215 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087215' /scratch/stefan/7774412/working/building/REAL300004087215 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087215 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087215/0 /scratch/stefan/7774412/working/building/REAL300004087215 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/275 `/scratch/stefan/7774412/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=NSN=C2N2CCOCC2)S1) `REAL300004087215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087215 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=NSN=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 8, 14, 8, 1, 8, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 99, 115, 115, 69, 69, 69, 40, 68, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 69, 69, 69, 69, 99, 99, 69, 40, 40, 6, 6, 6, 6, 6, 6, 6, 6] 162 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 462 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: REAL300004087215 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=NSN=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 8, 14, 8, 1, 8, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 9, 31, 69, 69, 69, 69, 69, 118, 118, 118, 118, 118, 1, 2, 2, 2, 3, 3, 2, 9, 9, 118, 118, 118, 118, 118, 118, 118, 118] 162 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 222 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087215 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=NSN=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 8, 14, 8, 1, 8, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 162, 162, 162, 118, 118, 118, 90, 118, 30, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 162, 162, 118, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1] 162 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 626 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087215 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087215/1 /scratch/stefan/7774412/working/building/REAL300004087215 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/276 `/scratch/stefan/7774412/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=NSN=C2N2CCOCC2)S1) `REAL300004087215.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087215 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=NSN=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 8, 14, 8, 1, 8, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 145, 152, 152, 102, 28, 24, 22, 24, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 102, 102, 102, 102, 145, 145, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6] 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: 470 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087215 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=NSN=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 8, 14, 8, 1, 8, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 22, 22, 38, 49, 102, 102, 102, 102, 102, 176, 176, 176, 176, 176, 1, 2, 2, 2, 2, 2, 38, 38, 176, 176, 176, 176, 176, 176, 176, 176] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 367 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087215 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=NSN=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 8, 14, 8, 1, 8, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 201, 201, 201, 176, 66, 59, 55, 59, 31, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 201, 201, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 494 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087215 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087215 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087215/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087215/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087215 Building REAL300004087216 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087216' /scratch/stefan/7774412/working/building/REAL300004087216 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087216 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087216/0 /scratch/stefan/7774412/working/building/REAL300004087216 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/277 `/scratch/stefan/7774412/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CNC2=CC=C(S(C)(=O)=O)C=C2)S1) `REAL300004087216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087216 none CC1=C(CC(=O)[O-])N=C(NC(=O)CNC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 24, 25, 25, 15, 15, 15, 13, 15, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 15, 15, 15, 15, 24, 24, 15, 13, 13, 4, 1, 1, 3, 3, 3, 1, 1] 27 rigid atoms, others: [34, 35, 39, 40, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087216 none CC1=C(CC(=O)[O-])N=C(NC(=O)CNC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 4, 10, 15, 15, 10, 11, 24, 24, 24, 15, 15, 1, 2, 2, 2, 2, 2, 2, 4, 4, 10, 15, 15, 24, 24, 24, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 138 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087216 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087216/1 /scratch/stefan/7774412/working/building/REAL300004087216 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/278 `/scratch/stefan/7774412/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNC2=CC=C(S(C)(=O)=O)C=C2)S1) `REAL300004087216.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087216/1/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: REAL300004087216 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 181, 187, 187, 152, 82, 34, 10, 34, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 152, 152, 152, 152, 181, 181, 10, 10, 4, 1, 1, 3, 3, 3, 1, 1] 201 rigid atoms, others: [33, 34, 38, 39, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 479 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087216 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CNC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 38, 38, 102, 128, 152, 152, 128, 128, 181, 181, 181, 152, 152, 1, 2, 2, 2, 2, 2, 102, 102, 128, 152, 152, 181, 181, 181, 152, 152] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 862 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087216 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087216 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087216/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087216/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087216 Building REAL300004087217 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087217' /scratch/stefan/7774412/working/building/REAL300004087217 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087217 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087217/0 /scratch/stefan/7774412/working/building/REAL300004087217 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/279 `/scratch/stefan/7774412/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(C(F)(F)F)C=C3N2)S1) `REAL300004087217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087217 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(C(F)(F)F)C=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 15, 27, 27, 27, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 27, 27, 11, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087217 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(C(F)(F)F)C=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 15, 15, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087217 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087217 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087217/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087217 Building REAL300004087218 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087218' /scratch/stefan/7774412/working/building/REAL300004087218 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087218 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087218/0 /scratch/stefan/7774412/working/building/REAL300004087218 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/280 `/scratch/stefan/7774412/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)OC2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087218 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)OC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 160, 160, 160, 112, 78, 78, 20, 78, 7, 20, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 112, 112, 112, 112, 160, 160, 78, 20, 20, 20, 20, 1, 1, 1, 1] 160 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 570 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: REAL300004087218 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)OC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 21, 19, 77, 112, 112, 77, 77, 112, 112, 112, 112, 112, 1, 2, 2, 2, 2, 2, 3, 21, 21, 21, 21, 112, 112, 112, 112] 160 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 497 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087218 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087218/1 /scratch/stefan/7774412/working/building/REAL300004087218 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/281 `/scratch/stefan/7774412/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)OC2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087218.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087218/1/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: REAL300004087218 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)OC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [167, 167, 167, 167, 201, 201, 201, 167, 88, 37, 12, 37, 5, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 167, 167, 167, 167, 201, 201, 12, 12, 12, 12, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 517 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087218 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)OC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 39, 39, 66, 66, 137, 167, 167, 156, 167, 167, 167, 167, 167, 167, 1, 2, 2, 2, 2, 2, 66, 66, 66, 66, 167, 167, 167, 167] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 465 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087218 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087218 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087218/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087218/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087218 Building REAL300004087219 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087219' /scratch/stefan/7774412/working/building/REAL300004087219 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087219 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087219/0 /scratch/stefan/7774412/working/building/REAL300004087219 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/282 `/scratch/stefan/7774412/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCOC2=CC=C(C)C=C2C)S1) `REAL300004087219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087219 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCOC2=CC=C(C)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 201, 201, 201, 132, 132, 132, 122, 132, 62, 42, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 201, 201, 132, 116, 116, 71, 71, 42, 42, 1, 1, 2, 2, 2, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45]) total number of confs: 1028 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087219 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCOC2=CC=C(C)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 4, 6, 12, 60, 132, 132, 60, 60, 132, 132, 132, 1, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 12, 12, 132, 132, 132, 132, 132, 132, 132, 132, 132] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 781 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087219 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087219 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087219/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087219 Building REAL300004087220 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087220' /scratch/stefan/7774412/working/building/REAL300004087220 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087220 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087220/0 /scratch/stefan/7774412/working/building/REAL300004087220 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/283 `/scratch/stefan/7774412/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N(C)C)=NC3=CC=CC=C32)S1) `REAL300004087220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087220 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N(C)C)=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 39, 55, 55, 20, 12, 10, 1, 10, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 39, 39, 12, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1] 55 rigid atoms, others: [32, 39, 40, 41, 10, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 237 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087220 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N(C)C)=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 20, 20, 36, 36, 19, 20, 20, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 20, 36, 36, 36, 36, 36, 36, 20, 20, 20, 20] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087220 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087220 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087220/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087220 Building REAL300004087221 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087221' /scratch/stefan/7774412/working/building/REAL300004087221 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087221 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087221/0 /scratch/stefan/7774412/working/building/REAL300004087221 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/284 `/scratch/stefan/7774412/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3=CC=C(C)C(C)=C3)=C2)S1) `REAL300004087221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087221 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3=CC=C(C)C(C)=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 24, 25, 25, 15, 12, 12, 1, 12, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 1, 15, 16, 16, 16, 24, 24, 12, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 107 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087221 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3=CC=C(C)C(C)=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 16, 67, 67, 67, 67, 67, 67, 67, 15, 1, 2, 2, 2, 2, 2, 2, 15, 67, 67, 67, 67, 67, 67, 67, 67, 67, 15] 107 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 118 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087221 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3=CC=C(C)C(C)=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 107, 107, 107, 67, 55, 55, 11, 55, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 67, 67, 67, 67, 107, 107, 55, 11, 1, 1, 2, 2, 2, 2, 2, 2, 1, 11] 107 rigid atoms, others: [33, 34, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 388 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087221 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087221 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087221/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087221 Building REAL300004087222 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087222' /scratch/stefan/7774412/working/building/REAL300004087222 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087222 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087222/0 /scratch/stefan/7774412/working/building/REAL300004087222 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/285 `/scratch/stefan/7774412/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(C)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087222 none CC1=NNC(C)=C1C(C)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 5, 8, 2, 2, 2, 1, 1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 2, 2, 2, 2, 2, 2] 13 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 55 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: REAL300004087222 none CC1=NNC(C)=C1C(C)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 37 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087222 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087222 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087222/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087222 Building REAL300004087223 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087223' /scratch/stefan/7774412/working/building/REAL300004087223 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087223 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087223/0 /scratch/stefan/7774412/working/building/REAL300004087223 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/286 `/scratch/stefan/7774412/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCC3)=N2)S1) `REAL300004087223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087223 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [12, 13, 13, 13, 22, 34, 34, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 13, 13, 13, 13, 22, 22, 10, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 55 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087223 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 12, 13, 13, 44, 44, 44, 44, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 44, 44, 44, 44, 44, 44, 44, 44] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087223 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(N3CCCC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 55, 55, 55, 44, 35, 35, 12, 35, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 44, 44, 44, 44, 55, 55, 35, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1] 55 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087223 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087223 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087223/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087223 Building REAL300004087224 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087224' /scratch/stefan/7774412/working/building/REAL300004087224 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087224 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087224/0 /scratch/stefan/7774412/working/building/REAL300004087224 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/287 `/scratch/stefan/7774412/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN(CC(F)(F)F)C2)S1) `REAL300004087224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087224 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN(CC(F)(F)F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 24, 24, 43, 55, 55, 24, 15, 13, 1, 13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 23, 24, 24, 24, 43, 43, 15, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1] 80 rigid atoms, others: [32, 33, 34, 35, 36, 39, 40, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 37, 38]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087224 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN(CC(F)(F)F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 24, 24, 24, 53, 53, 53, 53, 24, 1, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 24, 53, 53, 24, 24] 80 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087224 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087224 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087224/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087224 Building REAL300004087225 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087225' /scratch/stefan/7774412/working/building/REAL300004087225 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087225 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087225/0 /scratch/stefan/7774412/working/building/REAL300004087225 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/288 `/scratch/stefan/7774412/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)OC2=CC=C(Cl)C=C2)S1) `REAL300004087225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087225 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)OC2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 157, 157, 157, 111, 76, 76, 17, 76, 6, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 157, 157, 76, 17, 17, 17, 1, 1, 1, 1] 157 rigid atoms, others: [33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 545 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087225 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)OC2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 20, 20, 18, 75, 111, 111, 111, 111, 111, 111, 1, 2, 2, 2, 2, 2, 2, 21, 21, 21, 111, 111, 111, 111] 157 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087225 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087225/1 /scratch/stefan/7774412/working/building/REAL300004087225 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/289 `/scratch/stefan/7774412/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H](C)OC2=CC=C(Cl)C=C2)S1) `REAL300004087225.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087225/1/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: REAL300004087225 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H](C)OC2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 201, 201, 201, 173, 95, 47, 16, 47, 7, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 201, 201, 16, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 492 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: REAL300004087225 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H](C)OC2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 12, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 32, 32, 63, 63, 63, 141, 173, 173, 162, 163, 173, 173, 1, 2, 2, 2, 2, 2, 63, 63, 63, 173, 173, 173, 173] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 459 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087225 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087225 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087225/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087225/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087225 Building REAL300004087226 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087226' /scratch/stefan/7774412/working/building/REAL300004087226 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087226 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087226/0 /scratch/stefan/7774412/working/building/REAL300004087226 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/290 `/scratch/stefan/7774412/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C2=CC=CC=C2)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087226 none CC1=CN(C2=CC=CC=C2)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 13, 14, 14, 15, 15, 15, 23, 23, 23, 15, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 14, 23, 23, 15, 15, 15] 23 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087226 none CC1=CN(C2=CC=CC=C2)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 1, 1, 1, 9, 9, 9, 14, 14, 15, 23, 23, 23, 14, 14, 14, 2, 2, 2, 1, 3, 4, 1, 4, 4, 9, 23, 23, 15, 15, 15] 23 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 28] set([5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087226 none CC1=CN(C2=CC=CC=C2)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 15, 15, 14, 14, 14, 15, 15, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 59 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087226 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087226 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087226/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087226 Building REAL300004087227 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087227' /scratch/stefan/7774412/working/building/REAL300004087227 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087227 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087227/0 /scratch/stefan/7774412/working/building/REAL300004087227 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/291 `/scratch/stefan/7774412/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2OC2=CC=CC=C2)S1) `REAL300004087227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087227 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2OC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 40, 58, 58, 22, 17, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 8, 14, 14, 22, 22, 22, 22, 40, 40, 17, 1, 1, 1, 14, 14, 9, 14, 14] 168 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087227 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2OC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 21, 22, 22, 22, 93, 95, 95, 93, 95, 95, 1, 2, 2, 2, 2, 2, 2, 22, 22, 22, 95, 95, 95, 95, 95] 168 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087227 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2OC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 168, 168, 168, 95, 84, 68, 14, 68, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 168, 168, 84, 14, 14, 14, 1, 1, 1, 1, 1] 168 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 669 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087227 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087227 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087227/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087227 Building REAL300004087228 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087228' /scratch/stefan/7774412/working/building/REAL300004087228 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087228 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087228/0 /scratch/stefan/7774412/working/building/REAL300004087228 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/292 `/scratch/stefan/7774412/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1) `REAL300004087228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087228 none CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 13, 13, 13, 19, 19, 13, 19, 19, 13, 13, 13, 6, 6, 2, 2, 2, 2, 2, 2, 13, 19, 19, 13, 19, 19] 23 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 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: 64 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087228 none CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 19, 19, 19, 13, 13, 13, 1, 1, 1, 5, 5, 1, 5, 5, 2, 2, 2, 8, 8, 13, 19, 19, 13, 13, 13, 1, 5, 5, 1, 5, 5] 23 rigid atoms, others: [0, 1, 2, 3, 4, 37, 18, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087228 none CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 15, 19, 19, 19, 19, 19, 19, 23, 23, 23, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 19, 23, 23, 19, 19, 19, 5, 1, 1, 1, 1, 1] 23 rigid atoms, others: [38, 39, 40, 41, 42, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087228 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087228/1 /scratch/stefan/7774412/working/building/REAL300004087228 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/293 `/scratch/stefan/7774412/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1) `REAL300004087228.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087228 none CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 87, 35, 8, 35, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 118, 118, 118, 155, 155, 147, 155, 155, 118, 118, 118, 87, 87, 3, 3, 2, 2, 2, 118, 155, 155, 148, 155, 155] 201 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 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: 471 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087228 none CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 21, 21, 47, 118, 118, 118, 178, 201, 201, 118, 118, 118, 1, 1, 1, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 178, 178, 118, 118, 118, 1, 4, 4, 2, 4, 4] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087228 none CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 4, 16, 48, 48, 84, 155, 155, 155, 201, 201, 201, 155, 155, 155, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 201, 201, 155, 155, 155, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 585 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087228 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087228 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087228/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087228/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087228 Building REAL300004087229 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087229' /scratch/stefan/7774412/working/building/REAL300004087229 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087229 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087229/0 /scratch/stefan/7774412/working/building/REAL300004087229 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/294 `/scratch/stefan/7774412/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(OC2=CC=CC=C2)C(C)(C)O)S1) `REAL300004087229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087229 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(OC2=CC=CC=C2)C(C)(C)O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 513 conformations in input total number of sets (complete confs): 513 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 129, 148, 148, 74, 50, 50, 16, 50, 7, 1, 1, 1, 1, 1, 1, 1, 16, 36, 36, 38, 74, 74, 74, 74, 129, 129, 50, 16, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 114] 513 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 825 number of broken/clashed sets: 93 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087229 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(OC2=CC=CC=C2)C(C)(C)O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 513 conformations in input total number of sets (complete confs): 513 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 45, 74, 74, 45, 74, 74, 17, 29, 28, 31, 1, 2, 2, 2, 2, 2, 2, 17, 74, 74, 45, 74, 74, 32, 32, 32, 32, 32, 32, 96] 513 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 437 number of broken/clashed sets: 93 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087229 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087229/1 /scratch/stefan/7774412/working/building/REAL300004087229 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/295 `/scratch/stefan/7774412/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(OC2=CC=CC=C2)C(C)(C)O)S1) `REAL300004087229.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087229/1/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: REAL300004087229 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(OC2=CC=CC=C2)C(C)(C)O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 37, 40, 40, 33, 24, 15, 9, 15, 6, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 33, 33, 33, 33, 37, 37, 9, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 63] 129 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 234 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087229 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(OC2=CC=CC=C2)C(C)(C)O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 7, 13, 13, 14, 24, 33, 33, 30, 33, 33, 14, 22, 22, 22, 1, 2, 2, 2, 2, 2, 14, 33, 33, 30, 33, 33, 22, 22, 22, 22, 22, 22, 66] 129 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087229 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087229 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087229/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087229/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087229 Building REAL300004087230 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087230' /scratch/stefan/7774412/working/building/REAL300004087230 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087230 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087230/0 /scratch/stefan/7774412/working/building/REAL300004087230 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/296 `/scratch/stefan/7774412/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)(C)C)C(Cl)=C2)S1) `REAL300004087230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087230 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)(C)C)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1] 25 rigid atoms, others: [41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087230 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)(C)C)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 12, 12, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087230 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087230 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087230/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087230 Building REAL300004087231 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087231' /scratch/stefan/7774412/working/building/REAL300004087231 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087231 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087231/0 /scratch/stefan/7774412/working/building/REAL300004087231 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/297 `/scratch/stefan/7774412/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)CCCCC3=O)S1) `REAL300004087231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087231 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)CCCCC3=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 20, 20, 20, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087231 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)CCCCC3=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 11, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 20 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087231 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087231 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087231/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087231 Building REAL300004087232 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087232' /scratch/stefan/7774412/working/building/REAL300004087232 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087232 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087232/0 /scratch/stefan/7774412/working/building/REAL300004087232 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/298 `/scratch/stefan/7774412/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NC=CN3C2)S1) `REAL300004087232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087232 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NC=CN3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 25, 26, 26, 15, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 16, 16, 16, 25, 25, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087232 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NC=CN3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087232 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087232 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087232/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087232 Building REAL300004087233 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087233' /scratch/stefan/7774412/working/building/REAL300004087233 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087233 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087233/0 /scratch/stefan/7774412/working/building/REAL300004087233 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/299 `/scratch/stefan/7774412/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(CC3=CC=CC=C3)=C2)S1) `REAL300004087233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087233 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(CC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 29, 46, 46, 16, 13, 13, 1, 13, 1, 1, 1, 1, 1, 9, 19, 19, 12, 19, 19, 1, 16, 16, 16, 16, 29, 29, 13, 1, 9, 9, 19, 19, 19, 19, 19, 1] 149 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 241 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087233 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(CC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 69, 88, 88, 85, 88, 88, 16, 1, 2, 2, 2, 2, 2, 2, 16, 69, 69, 88, 88, 88, 88, 88, 16] 149 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 296 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087233 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(CC3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 149, 149, 149, 88, 72, 72, 19, 72, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 1, 19, 88, 88, 88, 88, 149, 149, 72, 19, 4, 4, 1, 1, 1, 1, 1, 19] 149 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087233 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087233 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087233/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087233 Building REAL300004087234 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087234' /scratch/stefan/7774412/working/building/REAL300004087234 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087234 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087234/0 /scratch/stefan/7774412/working/building/REAL300004087234 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/300 `/scratch/stefan/7774412/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=C(O)C=C2)C2CC2)S1) `REAL300004087234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087234 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=C(O)C=C2)C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 21, 21, 21, 13, 13, 13, 5, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 13, 13, 13, 13, 21, 21, 13, 5, 5, 3, 1, 1, 2, 1, 1, 6, 6, 6, 6, 6] 46 rigid atoms, others: [34, 35, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087234 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=C(O)C=C2)C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 8, 13, 13, 13, 13, 13, 13, 13, 13, 15, 15, 1, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 13, 26, 13, 13, 15, 15, 15, 15, 15] 46 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087234 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=C(O)C=C2)C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 23, 23, 23, 15, 15, 15, 9, 15, 4, 1, 4, 6, 6, 4, 4, 6, 6, 1, 1, 1, 15, 15, 15, 15, 23, 23, 15, 9, 9, 4, 6, 6, 12, 6, 6, 1, 1, 1, 1, 1] 46 rigid atoms, others: [39, 40, 41, 42, 43, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087234 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087234 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087234/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087234 Building REAL300004087235 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087235' /scratch/stefan/7774412/working/building/REAL300004087235 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087235 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087235/0 /scratch/stefan/7774412/working/building/REAL300004087235 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/301 `/scratch/stefan/7774412/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(CC3=CC=CC=C3)N(C)N=C2)S1) `REAL300004087235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087235 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(CC3=CC=CC=C3)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [24, 25, 25, 25, 45, 65, 65, 25, 14, 12, 1, 12, 1, 1, 1, 7, 11, 11, 7, 11, 11, 1, 1, 1, 1, 24, 25, 25, 25, 45, 45, 14, 7, 7, 11, 11, 7, 11, 11, 2, 2, 2, 1] 151 rigid atoms, others: [10, 12, 13, 14, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087235 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(CC3=CC=CC=C3)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 25, 25, 73, 91, 91, 73, 91, 91, 25, 25, 25, 25, 1, 2, 2, 2, 2, 2, 2, 73, 73, 91, 91, 73, 91, 91, 25, 25, 25, 25] 151 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087235 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(CC3=CC=CC=C3)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 151, 151, 151, 91, 74, 68, 11, 68, 11, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 91, 91, 91, 91, 151, 151, 74, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11] 151 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42]) total number of confs: 574 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087235 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087235 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087235/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087235 Building REAL300004087236 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087236' /scratch/stefan/7774412/working/building/REAL300004087236 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087236 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087236/0 /scratch/stefan/7774412/working/building/REAL300004087236 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/302 `/scratch/stefan/7774412/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN3C=CN=C3C2)S1) `REAL300004087236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087236 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN3C=CN=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 13, 13, 13, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087236 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN3C=CN=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087236 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087236 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087236/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087236 Building REAL300004087237 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087237' /scratch/stefan/7774412/working/building/REAL300004087237 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087237 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087237/0 /scratch/stefan/7774412/working/building/REAL300004087237 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/303 `/scratch/stefan/7774412/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=CN=CN3C2)S1) `REAL300004087237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087237 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=CN=CN3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 26, 27, 27, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087237 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=CN=CN3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087237 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087237 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087237/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087237 Building REAL300004087238 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087238' /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004087238 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087238/0 /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/304 `/scratch/stefan/7774412/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)[N-]C=N2)S1) `REAL300004087238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)[N-]C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 13, 13, 23, 35, 35, 13, 9, 9, 1, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 12, 13, 13, 13, 23, 23, 10, 9, 9, 9, 9, 9, 1] 81 rigid atoms, others: [37, 10, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)[N-]C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 12, 13, 45, 45, 45, 45, 45, 45, 45, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 45, 45, 45, 45, 45, 12] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)[N-]C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 81, 81, 81, 45, 35, 35, 9, 35, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 45, 45, 45, 45, 81, 81, 35, 1, 1, 1, 1, 1, 9] 81 rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 317 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087238/1 /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/305 `/scratch/stefan/7774412/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)N=C[N-]2)S1) `REAL300004087238.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)N=C[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 11, 21, 33, 33, 11, 7, 7, 1, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 10, 11, 11, 11, 21, 21, 8, 9, 9, 9, 9, 9, 1] 79 rigid atoms, others: [37, 10, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)N=C[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 10, 10, 43, 43, 43, 43, 43, 43, 43, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 43, 43, 43, 43, 43, 10] 79 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)N=C[N-]2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 79, 79, 79, 43, 32, 32, 9, 32, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 43, 43, 43, 79, 79, 32, 1, 1, 1, 1, 1, 9] 79 rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37]) total number of confs: 313 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087238/2 /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/306 `/scratch/stefan/7774412/working/3D/306' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)NC=N2)S1) `REAL300004087238.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 26, 26, 47, 71, 71, 26, 16, 12, 1, 12, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 25, 26, 26, 26, 47, 47, 17, 7, 7, 7, 7, 7, 1, 1] 132 rigid atoms, others: [37, 38, 10, 12, 13, 14, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 299 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 25, 26, 78, 78, 78, 78, 78, 78, 78, 25, 25, 25, 1, 2, 2, 2, 2, 2, 2, 78, 78, 78, 78, 78, 25, 26] 132 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087238 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(=O)C3=CC=CC=C3)NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 132, 132, 132, 78, 58, 53, 7, 53, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 78, 78, 78, 78, 132, 132, 58, 1, 1, 1, 1, 1, 7, 7] 132 rigid atoms, others: [32, 33, 34, 35, 36, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 499 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087238 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087238 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087238/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087238/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087238/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087238 Building REAL300004087239 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087239' /scratch/stefan/7774412/working/building/REAL300004087239 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087239 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087239/0 /scratch/stefan/7774412/working/building/REAL300004087239 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/307 `/scratch/stefan/7774412/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](CC(C)C)NCC(F)(F)F)S1) `REAL300004087239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087239 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](CC(C)C)NCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 20, 20, 31, 31, 31, 20, 44, 66, 66, 66, 66, 1, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 31, 31, 44, 66, 66] 121 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 353 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087239 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087239/1 /scratch/stefan/7774412/working/building/REAL300004087239 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/308 `/scratch/stefan/7774412/working/3D/308' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H](CC(C)C)NCC(F)(F)F)S1) `REAL300004087239.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087239/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087239 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H](CC(C)C)NCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 10, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 10, 29, 29, 48, 48, 55, 55, 55, 48, 117, 132, 132, 132, 132, 1, 2, 2, 2, 2, 2, 55, 55, 55, 55, 55, 55, 55, 55, 55, 117, 132, 132] 145 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 520 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087239 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087239 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087239/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087239/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087239 Building REAL300004087240 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087240' /scratch/stefan/7774412/working/building/REAL300004087240 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087240 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087240/0 /scratch/stefan/7774412/working/building/REAL300004087240 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/309 `/scratch/stefan/7774412/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCCCS(N)(=O)=O)S1) `REAL300004087240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087240 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCCCS(N)(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 14, 8, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087240 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087240 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087240/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087240 Building REAL300004087241 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087241' /scratch/stefan/7774412/working/building/REAL300004087241 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087241 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087241/0 /scratch/stefan/7774412/working/building/REAL300004087241 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/310 `/scratch/stefan/7774412/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC(F)F)N=C2)S1) `REAL300004087241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087241 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC(F)F)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 3, 3, 3, 1] 3 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087241 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OCC(F)F)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087241 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087241 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087241/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087241 Building REAL300004087242 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087242' /scratch/stefan/7774412/working/building/REAL300004087242 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087242 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087242/0 /scratch/stefan/7774412/working/building/REAL300004087242 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/311 `/scratch/stefan/7774412/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)C(F)(F)F)C=C2)S1) `REAL300004087242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087242 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 12, 15, 15, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 7, 7, 7, 7, 12, 12, 5, 1, 1, 6, 6, 6, 6, 1, 1] 31 rigid atoms, others: [32, 37, 38, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087242 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 7, 7, 5, 7, 18, 18, 18, 18, 18, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 18, 18, 18, 18, 7, 7] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087242 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087242 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087242/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087242 Building REAL300004087243 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087243' /scratch/stefan/7774412/working/building/REAL300004087243 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087243 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087243/0 /scratch/stefan/7774412/working/building/REAL300004087243 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/312 `/scratch/stefan/7774412/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(OCC(F)F)C=N2)S1) `REAL300004087243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087243 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(OCC(F)F)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 1] 3 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087243 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(OCC(F)F)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087243 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087243 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087243/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087243 Building REAL300004087244 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087244' /scratch/stefan/7774412/working/building/REAL300004087244 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087244 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087244/0 /scratch/stefan/7774412/working/building/REAL300004087244 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/313 `/scratch/stefan/7774412/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3CCOCC3)CC2)S1) `REAL300004087244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087244 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 31, 31, 31, 16, 11, 11, 1, 11, 1, 1, 6, 6, 6, 6, 6, 1, 1, 16, 16, 16, 16, 31, 31, 11, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 31 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 129 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: REAL300004087244 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087244 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 31, 31, 31, 16, 13, 13, 6, 13, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 31, 31, 13, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 31 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39]) total number of confs: 129 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087244 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087244/1 /scratch/stefan/7774412/working/building/REAL300004087244 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/314 `/scratch/stefan/7774412/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3CCOCC3)CC2)S1) `REAL300004087244.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087244 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 154, 154, 201, 201, 201, 154, 46, 10, 1, 10, 1, 1, 4, 4, 4, 4, 4, 1, 1, 154, 154, 154, 154, 201, 201, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 10, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087244 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 62, 62, 154, 166, 166, 166, 166, 166, 154, 154, 1, 2, 2, 2, 2, 2, 166, 166, 166, 166, 166, 166, 166, 166, 154, 154, 154, 154] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 454 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087244 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 78, 20, 4, 20, 1, 1, 1, 1, 1, 1, 1, 4, 4, 166, 166, 166, 166, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38]) total number of confs: 467 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087244 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087244 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087244/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087244/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087244 Building REAL300004087245 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087245' /scratch/stefan/7774412/working/building/REAL300004087245 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087245 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087245/0 /scratch/stefan/7774412/working/building/REAL300004087245 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/315 `/scratch/stefan/7774412/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(C(C)(C)O)CC2)S1) `REAL300004087245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087245 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(C(C)(C)O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 32, 33, 33, 16, 12, 10, 1, 10, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 16, 17, 17, 17, 32, 32, 12, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 12, 1, 1, 1, 1] 219 rigid atoms, others: [32, 33, 34, 44, 10, 43, 12, 13, 14, 15, 16, 42, 20, 21, 45, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087245 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(C(C)(C)O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 22, 22, 40, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 22, 40, 40, 22, 40, 40, 120, 16, 16, 16, 16] 219 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 379 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087245 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087245 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087245/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087245 Building REAL300004087246 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087246' /scratch/stefan/7774412/working/building/REAL300004087246 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087246 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087246/0 /scratch/stefan/7774412/working/building/REAL300004087246 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/316 `/scratch/stefan/7774412/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1) `REAL300004087246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087246 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 41, 73, 73, 21, 12, 10, 1, 10, 1, 1, 10, 22, 22, 13, 13, 22, 22, 1, 1, 21, 21, 21, 21, 41, 41, 12, 22, 22, 22, 22, 1, 1, 1, 1] 181 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087246 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 21, 91, 108, 108, 97, 102, 108, 108, 21, 21, 1, 2, 2, 2, 2, 2, 3, 108, 108, 108, 108, 21, 21, 21, 21] 181 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087246 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 181, 181, 181, 108, 74, 67, 22, 67, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 108, 108, 108, 108, 181, 181, 74, 1, 1, 1, 1, 22, 22, 22, 22] 181 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 710 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087246 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087246/1 /scratch/stefan/7774412/working/building/REAL300004087246 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/317 `/scratch/stefan/7774412/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1) `REAL300004087246.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087246 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 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: [88, 88, 88, 88, 115, 130, 130, 88, 39, 11, 1, 11, 1, 1, 9, 16, 16, 11, 11, 16, 16, 1, 1, 88, 88, 88, 88, 115, 115, 16, 16, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087246 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 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, 2, 5, 5, 1, 1, 1, 13, 46, 46, 88, 155, 165, 165, 159, 163, 165, 165, 88, 88, 1, 2, 2, 2, 2, 2, 165, 165, 165, 165, 88, 88, 88, 88] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087246 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(OC3=CC=C(Cl)C=C3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 201, 201, 201, 165, 97, 53, 16, 53, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 165, 165, 165, 165, 201, 201, 1, 1, 1, 1, 16, 16, 16, 16] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 525 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087246 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087246 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087246/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087246/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087246 Building REAL300004087247 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087247' /scratch/stefan/7774412/working/building/REAL300004087247 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087247 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087247/0 /scratch/stefan/7774412/working/building/REAL300004087247 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/318 `/scratch/stefan/7774412/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CS(=O)(=O)C2)S1) `REAL300004087247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087247 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CS(=O)(=O)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 9, 9, 9, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 9, 9, 7, 5, 5, 1, 1, 1, 1, 1] 9 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087247 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CS(=O)(=O)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 14, 11, 11, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 6, 7, 7, 7, 7, 7, 1, 2, 2, 2, 3, 3, 2, 6, 6, 7, 7, 7, 7, 7] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087247 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087247 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087247/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087247 Building REAL300004087248 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087248' /scratch/stefan/7774412/working/building/REAL300004087248 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087248 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087248/0 /scratch/stefan/7774412/working/building/REAL300004087248 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/319 `/scratch/stefan/7774412/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN(C(C)C)C=C2)S1) `REAL300004087248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087248 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN(C(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 99, 109, 109, 57, 53, 51, 8, 51, 1, 1, 1, 1, 1, 11, 11, 1, 1, 57, 57, 57, 57, 99, 99, 53, 8, 8, 11, 11, 11, 11, 11, 11, 11, 1, 1] 128 rigid atoms, others: [37, 38, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087248 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN(C(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 21, 57, 57, 57, 94, 94, 57, 57, 1, 2, 2, 2, 2, 2, 2, 21, 21, 94, 94, 94, 94, 94, 94, 94, 57, 57] 128 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087248 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087248/1 /scratch/stefan/7774412/working/building/REAL300004087248 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/320 `/scratch/stefan/7774412/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN(C(C)C)C=C2)S1) `REAL300004087248.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087248/1/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: REAL300004087248 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN(C(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 68, 28, 6, 28, 1, 1, 1, 1, 1, 5, 5, 1, 1, 148, 148, 148, 148, 201, 201, 6, 6, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087248 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN(C(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 37, 37, 106, 148, 148, 148, 166, 166, 148, 148, 1, 2, 2, 2, 2, 2, 106, 106, 166, 166, 166, 166, 166, 166, 166, 148, 148] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087248 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087248 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087248/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087248/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087248 Building REAL300004087249 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087249' /scratch/stefan/7774412/working/building/REAL300004087249 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087249 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087249/0 /scratch/stefan/7774412/working/building/REAL300004087249 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/321 `/scratch/stefan/7774412/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N=C4C=CC=CN4C3=O)N2C)S1) `REAL300004087249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087249 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N=C4C=CC=CN4C3=O)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 8, 1, 1, 1, 1, 1, 2, 2, 2] 23 rigid atoms, others: [34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 40, 32, 41, 39, 33, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087249 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N=C4C=CC=CN4C3=O)N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087249 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087249 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087249/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087249 Building REAL300004087250 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087250' /scratch/stefan/7774412/working/building/REAL300004087250 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087250 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087250/0 /scratch/stefan/7774412/working/building/REAL300004087250 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/322 `/scratch/stefan/7774412/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC3=CC=CC=C3C=C2)S1) `REAL300004087250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087250 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC3=CC=CC=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 73, 73, 73, 42, 38, 38, 14, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 73, 73, 38, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 321 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087250 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC3=CC=CC=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 14, 22, 42, 42, 42, 42, 42, 42, 42, 42, 42, 1, 2, 2, 2, 2, 2, 2, 14, 14, 22, 22, 42, 42, 42, 42, 42, 42] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087250 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087250 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087250/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087250 Building REAL300004087251 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087251' /scratch/stefan/7774412/working/building/REAL300004087251 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087251 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087251/0 /scratch/stefan/7774412/working/building/REAL300004087251 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/323 `/scratch/stefan/7774412/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=C(N=CNC2=O)O1) `REAL300004087251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087251 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=C(N=CNC2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 8, 1, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 15, 15] 24 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087251 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=C(N=CNC2=O)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 8, 1, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 15, 15, 15, 24, 24, 24, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 24, 24, 15, 15, 15, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 33, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([32, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087251 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087251 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087251/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087251 Building REAL300004087252 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087252' /scratch/stefan/7774412/working/building/REAL300004087252 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087252 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087252/0 /scratch/stefan/7774412/working/building/REAL300004087252 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/324 `/scratch/stefan/7774412/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=CN=C2)S1) `REAL300004087252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087252 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 33, 33, 33, 19, 19, 17, 13, 17, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 19, 13, 13, 7, 7, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087252 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 6, 8, 19, 19, 18, 19, 19, 1, 2, 2, 2, 3, 3, 2, 6, 6, 8, 8, 19, 19, 18, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087252 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087252 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087252/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087252 Building REAL300004087253 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087253' /scratch/stefan/7774412/working/building/REAL300004087253 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087253 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087253/0 /scratch/stefan/7774412/working/building/REAL300004087253 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/325 `/scratch/stefan/7774412/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2N2CCCC2)S1) `REAL300004087253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087253 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 30, 32, 32, 17, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 30, 30, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 32 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300004087253 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 17, 17, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 20, 20, 20, 20, 20, 20, 20, 20] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087253 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2N2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 32, 32, 32, 20, 17, 16, 6, 16, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 32, 32, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 117 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087253 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087253 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087253/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087253 Building REAL300004087254 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087254' /scratch/stefan/7774412/working/building/REAL300004087254 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087254 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087254/0 /scratch/stefan/7774412/working/building/REAL300004087254 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/326 `/scratch/stefan/7774412/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC3=CC=CC=C3N2)S1) `REAL300004087254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087254 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC3=CC=CC=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 13, 13, 13, 11, 11, 11, 9, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 9, 9, 7, 7, 1, 1, 1, 1, 1] 13 rigid atoms, others: [34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087254 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NC3=CC=CC=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 4, 6, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 3, 3, 2, 4, 4, 6, 6, 11, 11, 11, 11, 11] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087254 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087254 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087254/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087254 Building REAL300004087255 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087255' /scratch/stefan/7774412/working/building/REAL300004087255 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087255 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087255/0 /scratch/stefan/7774412/working/building/REAL300004087255 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/327 `/scratch/stefan/7774412/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(F)C=C3S2)S1) `REAL300004087255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087255 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(F)C=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 14, 14, 27, 27, 27, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 27, 27, 10, 1, 1, 1, 1] 27 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087255 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(F)C=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 14, 14, 14, 14, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 13] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087255 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087255 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087255/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087255 Building REAL300004087256 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087256' /scratch/stefan/7774412/working/building/REAL300004087256 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087256 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087256/0 /scratch/stefan/7774412/working/building/REAL300004087256 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/328 `/scratch/stefan/7774412/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC3=CC=CC=C3S2)S1) `REAL300004087256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087256 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 201, 201, 201, 155, 155, 155, 144, 155, 47, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 201, 201, 155, 144, 144, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 800 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087256 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 16, 54, 155, 155, 155, 155, 155, 155, 155, 155, 1, 2, 2, 2, 2, 2, 2, 6, 6, 54, 54, 155, 155, 155, 155] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 334 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087256 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087256/1 /scratch/stefan/7774412/working/building/REAL300004087256 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/329 `/scratch/stefan/7774412/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC3=CC=CC=C3S2)S1) `REAL300004087256.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087256/1/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: REAL300004087256 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 196, 196, 196, 201, 201, 201, 196, 170, 132, 75, 132, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 201, 201, 75, 75, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087256 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 8, 23, 23, 40, 55, 122, 196, 196, 196, 196, 196, 196, 196, 196, 1, 2, 2, 2, 2, 2, 40, 40, 122, 122, 196, 196, 196, 196] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 612 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087256 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087256 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087256/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087256/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087256 Building REAL300004087257 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087257' /scratch/stefan/7774412/working/building/REAL300004087257 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087257 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087257/0 /scratch/stefan/7774412/working/building/REAL300004087257 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/330 `/scratch/stefan/7774412/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCCC3)=CC=N2)S1) `REAL300004087257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087257 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCCC3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 19, 30, 36, 36, 18, 13, 9, 1, 9, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 18, 19, 19, 19, 29, 30, 13, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 51 rigid atoms, others: [39, 40, 10, 12, 13, 14, 15, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087257 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCCC3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 34, 34, 34, 34, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 34, 34, 34, 34, 34, 34, 34, 34, 18, 18] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087257 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3CCCC3)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 51, 51, 51, 34, 27, 23, 5, 23, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 34, 34, 34, 34, 51, 51, 27, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 51 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40]) total number of confs: 182 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087257 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087257 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087257/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087257 Building REAL300004087258 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087258' /scratch/stefan/7774412/working/building/REAL300004087258 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087258 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087258/0 /scratch/stefan/7774412/working/building/REAL300004087258 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/331 `/scratch/stefan/7774412/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087258 none CNS(=O)(=O)C1=CC=C(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=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.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 3, 5, 5, 3, 2, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 11, 11, 11, 11, 2, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 3] 11 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087258 none CNS(=O)(=O)C1=CC=C(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=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.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 7, 7, 3, 3, 3, 1, 11, 11, 11, 11, 1, 1, 2, 2, 2, 3, 5, 5, 3, 3, 3, 1] 11 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 40, 24, 29, 30] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087258 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087258 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087258/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087258 Building REAL300004087259 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087259' /scratch/stefan/7774412/working/building/REAL300004087259 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087259 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087259/0 /scratch/stefan/7774412/working/building/REAL300004087259 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/332 `/scratch/stefan/7774412/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC3=CC=CC=C32)S1) `REAL300004087259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087259 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 9, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087259 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087259 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087259 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087259/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087259 Building REAL300004087260 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087260' /scratch/stefan/7774412/working/building/REAL300004087260 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087260 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087260/0 /scratch/stefan/7774412/working/building/REAL300004087260 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/333 `/scratch/stefan/7774412/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C3=CC=CC=C3N=C2C)S1) `REAL300004087260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087260 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C3=CC=CC=C3N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 12, 13, 13, 6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 12, 12, 4, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2] 13 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087260 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C3=CC=CC=C3N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087260 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087260 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087260/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087260 Building REAL300004087261 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087261' /scratch/stefan/7774412/working/building/REAL300004087261 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087261 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087261/0 /scratch/stefan/7774412/working/building/REAL300004087261 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/334 `/scratch/stefan/7774412/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(N(C)C)C=C2)S1) `REAL300004087261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087261 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 32, 34, 34, 17, 17, 16, 8, 16, 4, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 17, 17, 17, 17, 32, 32, 17, 8, 8, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1] 38 rigid atoms, others: [34, 35, 42, 43, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087261 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 15, 17, 17, 15, 15, 22, 22, 17, 17, 1, 2, 2, 2, 2, 2, 3, 9, 9, 15, 15, 17, 17, 22, 22, 22, 22, 22, 22, 17, 17] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087261 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087261 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087261/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087261 Building REAL300004087262 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087262' /scratch/stefan/7774412/working/building/REAL300004087262 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087262 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087262/0 /scratch/stefan/7774412/working/building/REAL300004087262 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/335 `/scratch/stefan/7774412/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C(O)C2=NC3=CC=CC=C3S2)S1) `REAL300004087262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087262 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C(O)C2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 67, 67, 67, 43, 34, 34, 26, 34, 11, 26, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 67, 67, 34, 26, 78, 11, 33, 1, 1, 1, 1] 603 rigid atoms, others: [36, 37, 38, 39, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 403 number of broken/clashed sets: 162 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087262 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C(O)C2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 11, 11, 22, 22, 43, 43, 43, 43, 43, 43, 43, 43, 1, 2, 2, 2, 3, 3, 2, 11, 33, 22, 66, 43, 43, 43, 43] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 242 number of broken/clashed sets: 162 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087262 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087262/1 /scratch/stefan/7774412/working/building/REAL300004087262 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/336 `/scratch/stefan/7774412/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C(O)C2=NC3=CC=CC=C3S2)S1) `REAL300004087262.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:2-3 Rotatable hydrogens reported. Reducing confs by a factor of 3 WARNING:root:Setting energy window to 12 and max confs to 66 ('energy: ', 12.0) ('conf: ', 66) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087262 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C(O)C2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 67, 67, 67, 65, 42, 30, 18, 30, 11, 18, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 67, 67, 18, 54, 11, 33, 1, 1, 1, 1] 603 rigid atoms, others: [35, 36, 37, 38, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 271 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087262 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C(O)C2=NC3=CC=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 26, 26, 26, 26, 39, 39, 65, 65, 65, 65, 65, 65, 65, 65, 1, 2, 2, 2, 2, 2, 26, 78, 39, 117, 65, 65, 65, 65] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087262 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087262 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087262/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087262/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087262 Building REAL300004087263 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087263' /scratch/stefan/7774412/working/building/REAL300004087263 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087263 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087263/0 /scratch/stefan/7774412/working/building/REAL300004087263 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/337 `/scratch/stefan/7774412/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=NC(C)=C2)ON=C3C(C)C)S1) `REAL300004087263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087263 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=NC(C)=C2)ON=C3C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 5, 1, 12, 8, 1, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 10, 10, 10, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 10, 10, 6, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2] 10 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087263 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=NC(C)=C2)ON=C3C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 5, 1, 12, 8, 1, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087263 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087263 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087263/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087263 Building REAL300004087264 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087264' /scratch/stefan/7774412/working/building/REAL300004087264 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087264 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087264/0 /scratch/stefan/7774412/working/building/REAL300004087264 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/338 `/scratch/stefan/7774412/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CC=N3)=N2)S1) `REAL300004087264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087264 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [12, 13, 13, 13, 25, 38, 38, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 13, 13, 13, 13, 25, 25, 10, 1, 11, 11, 11, 11] 56 rigid atoms, others: [10, 12, 13, 14, 15, 16, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087264 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 36, 36, 36, 36, 36, 13, 1, 2, 2, 2, 2, 2, 2, 13, 36, 36, 36, 36] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087264 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 56, 56, 56, 36, 29, 29, 11, 29, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 36, 36, 36, 36, 56, 56, 29, 11, 1, 1, 1, 1] 56 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 202 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087264 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087264 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087264/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087264 Building REAL300004087265 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087265' /scratch/stefan/7774412/working/building/REAL300004087265 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087265 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087265/0 /scratch/stefan/7774412/working/building/REAL300004087265 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/339 `/scratch/stefan/7774412/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1) `REAL300004087265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087265 none CC[NH+](CC)CC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 5, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2] 5 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 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: 53 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087265 none CC[NH+](CC)CC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 3, 3, 3, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 24, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 48 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087265 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087265/1 /scratch/stefan/7774412/working/building/REAL300004087265 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/340 `/scratch/stefan/7774412/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)CC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1) `REAL300004087265.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087265/1/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: REAL300004087265 none CCN(CC)CC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 91, 55, 91, 113, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 111, 111, 111, 111, 111, 113, 113, 113, 113, 113, 55, 55, 13, 13, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 579 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087265 none CCN(CC)CC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 30, 9, 30, 50, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 26, 37, 37, 13, 13, 13, 1, 48, 48, 48, 48, 48, 50, 50, 50, 50, 50, 9, 9, 1, 1, 10, 26, 26, 14, 14, 14] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 23, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 453 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087265 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087265 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087265/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087265/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087265 Building REAL300004087266 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087266' /scratch/stefan/7774412/working/building/REAL300004087266 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087266 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087266/0 /scratch/stefan/7774412/working/building/REAL300004087266 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/341 `/scratch/stefan/7774412/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC[NH+]2CCCC2)S1) `REAL300004087266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087266 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC[NH+]2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 17, 17, 17, 13, 13, 13, 13, 13, 7, 7, 5, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 13, 13, 13, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087266 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCC[NH+]2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 4, 4, 8, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087266 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087266 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087266/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087266 Building REAL300004087267 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087267' /scratch/stefan/7774412/working/building/REAL300004087267 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087267 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087267/0 /scratch/stefan/7774412/working/building/REAL300004087267 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/342 `/scratch/stefan/7774412/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN(C)C2=CC=CC=C2)S1) `REAL300004087267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087267 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN(C)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 62, 62, 62, 42, 38, 38, 14, 38, 3, 1, 3, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 62, 62, 38, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1] 62 rigid atoms, others: [33, 34, 35, 36, 37, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 238 number of broken/clashed sets: 62 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087267 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN(C)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 14, 41, 41, 42, 42, 41, 42, 42, 1, 2, 2, 2, 2, 2, 3, 14, 14, 41, 41, 41, 42, 42, 42, 42, 42] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 155 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087267 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087267/1 /scratch/stefan/7774412/working/building/REAL300004087267 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/343 `/scratch/stefan/7774412/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN(C)C2=CC=CC=C2)S1) `REAL300004087267.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087267/1/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: REAL300004087267 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN(C)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 201, 201, 201, 159, 92, 45, 13, 45, 3, 1, 3, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 201, 201, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 552 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087267 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN(C)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 37, 37, 107, 159, 159, 159, 159, 159, 159, 159, 1, 2, 2, 2, 2, 2, 107, 107, 159, 159, 159, 159, 159, 159, 159, 159] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 563 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087267 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087267 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087267/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087267/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087267 Building REAL300004087268 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087268' /scratch/stefan/7774412/working/building/REAL300004087268 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087268 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087268/0 /scratch/stefan/7774412/working/building/REAL300004087268 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/344 `/scratch/stefan/7774412/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=C(C)C=N3)CC2)S1) `REAL300004087268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087268 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=C(C)C=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 33, 33, 33, 19, 13, 11, 1, 11, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 19, 19, 19, 19, 33, 33, 12, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 56 rigid atoms, others: [32, 33, 34, 35, 36, 44, 10, 43, 12, 13, 14, 15, 16, 46, 23, 24, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087268 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=C(C)C=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 19, 19, 19, 19, 43, 43, 43, 43, 43, 43, 19, 19, 1, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 43, 43, 43, 43, 43, 43, 19, 19, 19, 19] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087268 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(C3=CC=C(C)C=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 5, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 56, 56, 56, 43, 31, 28, 6, 28, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 43, 43, 43, 43, 56, 56, 31, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 1, 6, 6, 6, 6] 56 rigid atoms, others: [37, 38, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087268 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087268 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087268/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087268 Building REAL300004087269 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087269' /scratch/stefan/7774412/working/building/REAL300004087269 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087269 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087269/0 /scratch/stefan/7774412/working/building/REAL300004087269 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/345 `/scratch/stefan/7774412/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN(C)CC2=CC=CC=C2)S1) `REAL300004087269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087269 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN(C)CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [39, 39, 39, 39, 63, 63, 63, 39, 38, 38, 19, 38, 9, 3, 9, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 63, 63, 38, 19, 19, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1] 63 rigid atoms, others: [36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300004087269 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN(C)CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 18, 18, 27, 39, 39, 35, 39, 39, 1, 2, 2, 2, 2, 2, 2, 12, 12, 18, 18, 18, 27, 27, 39, 39, 39, 39, 39] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087269 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087269 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087269/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087269 Building REAL300004087270 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087270' /scratch/stefan/7774412/working/building/REAL300004087270 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087270 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087270/0 /scratch/stefan/7774412/working/building/REAL300004087270 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/346 `/scratch/stefan/7774412/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N(C)C)=CC=N2)S1) `REAL300004087270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087270 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N(C)C)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 27, 27, 14, 9, 9, 1, 9, 1, 1, 1, 1, 7, 7, 1, 1, 1, 14, 15, 15, 15, 26, 26, 9, 1, 7, 7, 7, 7, 7, 7, 1, 1] 39 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087270 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N(C)C)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 5, 5, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 23, 23, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 23, 23, 23, 23, 23, 23, 14, 14] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087270 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087270 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087270/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087270 Building REAL300004087271 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087271' /scratch/stefan/7774412/working/building/REAL300004087271 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087271 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087271/0 /scratch/stefan/7774412/working/building/REAL300004087271 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/347 `/scratch/stefan/7774412/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087271 none CCCCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 88, 72, 28, 2, 28, 77, 3, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 96, 96, 96, 96, 96, 92, 92, 72, 72, 77, 77, 77, 77, 77, 7, 7, 2, 2, 2, 2, 2, 2, 7, 7] 201 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 676 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087271 none CCCCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 21, 7, 1, 7, 23, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 29, 29, 7, 7, 7, 1, 1, 29, 29, 29, 29, 29, 27, 27, 21, 21, 23, 23, 23, 23, 23, 1, 1, 7, 13, 13, 7, 7, 7, 1, 1] 201 rigid atoms, others: [4, 49, 7, 8, 9, 10, 11, 48, 40, 41, 24, 25] set([0, 1, 2, 3, 5, 6, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47]) total number of confs: 301 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087271 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087271 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087271/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087271 Building REAL300004087272 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087272' /scratch/stefan/7774412/working/building/REAL300004087272 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087272 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087272/0 /scratch/stefan/7774412/working/building/REAL300004087272 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/348 `/scratch/stefan/7774412/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087272 none CCCCN(C)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 102, 79, 25, 13, 25, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 111, 111, 111, 111, 111, 102, 102, 79, 79, 25, 25, 25, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 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: 510 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087272 none CCCCN(C)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 16, 12, 3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 45, 45, 13, 13, 13, 1, 1, 23, 23, 23, 23, 23, 16, 16, 12, 12, 3, 3, 3, 1, 1, 9, 25, 25, 13, 13, 13, 1, 1] 201 rigid atoms, others: [4, 37, 6, 7, 8, 9, 10, 45, 46, 23, 24, 38] set([0, 1, 2, 3, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 269 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087272 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087272 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087272/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087272 Building REAL300004087273 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087273' /scratch/stefan/7774412/working/building/REAL300004087273 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087273 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087273/0 /scratch/stefan/7774412/working/building/REAL300004087273 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/349 `/scratch/stefan/7774412/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1) `REAL300004087273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087273 none CCCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 91, 45, 7, 45, 91, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 99, 99, 99, 99, 99, 91, 91, 91, 91, 91, 91, 91, 7, 7, 2, 2, 2, 2, 2, 2, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 600 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087273 none CCCN(CC)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 11, 1, 11, 35, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 27, 27, 7, 7, 7, 1, 1, 37, 37, 37, 37, 37, 31, 31, 35, 35, 35, 35, 35, 1, 1, 7, 11, 11, 7, 7, 7, 1] 201 rigid atoms, others: [3, 37, 6, 7, 8, 9, 10, 45, 23, 24, 38] set([0, 1, 2, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 351 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087273 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087273 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087273/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087273 Building REAL300004087274 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087274' /scratch/stefan/7774412/working/building/REAL300004087274 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087274 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087274/0 /scratch/stefan/7774412/working/building/REAL300004087274 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/350 `/scratch/stefan/7774412/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1) `REAL300004087274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087274 none CC(=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [11, 1, 11, 11, 31, 31, 33, 33, 33, 33, 45, 45, 45, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 33, 45, 45, 33, 33, 33, 1, 1, 1, 1] 45 rigid atoms, others: [1, 34, 35, 36, 33, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 161 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: REAL300004087274 none CC(=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 10, 33, 33, 31, 33, 33, 33, 10, 10, 10, 10, 2, 3, 3, 2, 2, 2, 33, 33, 33, 33] 45 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087274 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087274 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087274/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087274 Building REAL300004087275 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087275' /scratch/stefan/7774412/working/building/REAL300004087275 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087275 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087275/0 /scratch/stefan/7774412/working/building/REAL300004087275 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/351 `/scratch/stefan/7774412/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NN(C)C=C2)S1) `REAL300004087275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087275 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 58, 58, 58, 33, 33, 33, 16, 33, 8, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 58, 58, 33, 16, 16, 8, 8, 2, 2, 2, 1, 1] 58 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087275 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 10, 16, 33, 33, 33, 33, 33, 1, 2, 2, 2, 3, 3, 2, 10, 10, 16, 16, 33, 33, 33, 33, 33] 58 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087275 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087275 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087275/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087275 Building REAL300004087276 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087276' /scratch/stefan/7774412/working/building/REAL300004087276 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087276 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087276/0 /scratch/stefan/7774412/working/building/REAL300004087276 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/352 `/scratch/stefan/7774412/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CO3)N2)S1) `REAL300004087276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087276 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CO3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 24, 25, 25, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 24, 24, 10, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087276 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CO3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087276 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087276 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087276/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087276 Building REAL300004087277 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087277' /scratch/stefan/7774412/working/building/REAL300004087277 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087277 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087277/0 /scratch/stefan/7774412/working/building/REAL300004087277 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/353 `/scratch/stefan/7774412/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=C(C)C=CN3N=C2)S1) `REAL300004087277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087277 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=C(C)C=CN3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 18, 18, 18, 34, 34, 34, 18, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 34, 34, 13, 1, 2, 2, 2, 1, 1, 1] 34 rigid atoms, others: [33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087277 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=C(C)C=CN3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18] 34 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087277 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087277 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087277/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087277 Building REAL300004087278 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087278' /scratch/stefan/7774412/working/building/REAL300004087278 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087278 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087278/0 /scratch/stefan/7774412/working/building/REAL300004087278 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/354 `/scratch/stefan/7774412/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)N=NS2)S1) `REAL300004087278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087278 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)N=NS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 25, 25, 48, 59, 59, 25, 13, 11, 1, 11, 1, 1, 1, 9, 9, 1, 1, 1, 24, 25, 25, 25, 48, 48, 13, 9, 9, 9, 9, 9] 80 rigid atoms, others: [10, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087278 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)N=NS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 25, 49, 49, 24, 24, 24, 1, 2, 2, 2, 2, 2, 2, 49, 49, 49, 49, 49] 80 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087278 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)N=NS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 80, 80, 80, 49, 35, 33, 9, 33, 9, 1, 1, 1, 1, 9, 9, 8, 49, 49, 49, 49, 80, 80, 35, 1, 1, 1, 1, 1] 80 rigid atoms, others: [13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 297 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087278 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087278 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087278/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087278 Building REAL300004087279 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087279' /scratch/stefan/7774412/working/building/REAL300004087279 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087279 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087279/0 /scratch/stefan/7774412/working/building/REAL300004087279 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/355 `/scratch/stefan/7774412/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3NC=CC3=C2)S1) `REAL300004087279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087279 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3NC=CC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087279 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3NC=CC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087279 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087279 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087279/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087279 Building REAL300004087280 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087280' /scratch/stefan/7774412/working/building/REAL300004087280 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087280 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087280/0 /scratch/stefan/7774412/working/building/REAL300004087280 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/356 `/scratch/stefan/7774412/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NNC=C3)S2)S1) `REAL300004087280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087280 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NNC=C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 17, 17, 29, 31, 31, 17, 12, 12, 1, 12, 1, 1, 1, 1, 1, 10, 10, 10, 10, 1, 16, 17, 17, 17, 29, 29, 12, 1, 1, 10, 10, 10] 53 rigid atoms, others: [10, 12, 13, 14, 15, 16, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087280 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NNC=C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 35, 35, 35, 35, 16, 1, 2, 2, 2, 2, 2, 2, 17, 17, 35, 35, 35] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087280 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NNC=C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 36, 53, 53, 53, 35, 28, 28, 10, 28, 10, 10, 10, 1, 1, 1, 1, 1, 1, 10, 35, 36, 36, 36, 53, 53, 28, 10, 10, 1, 1, 1] 53 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 187 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087280 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087280 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087280/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087280 Building REAL300004087281 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087281' /scratch/stefan/7774412/working/building/REAL300004087281 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087281 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087281/0 /scratch/stefan/7774412/working/building/REAL300004087281 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/357 `/scratch/stefan/7774412/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2CC(F)(F)F)S1) `REAL300004087281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087281 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2CC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 37, 66, 66, 21, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 21, 21, 21, 21, 37, 37, 14, 1, 1, 6, 6] 108 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) 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: REAL300004087281 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2CC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 21, 21, 21, 21, 21, 67, 67, 67, 67, 1, 2, 2, 2, 2, 2, 2, 21, 21, 67, 67] 108 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087281 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087281 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087281/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087281 Building REAL300004087282 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087282' /scratch/stefan/7774412/working/building/REAL300004087282 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087282 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087282/0 /scratch/stefan/7774412/working/building/REAL300004087282 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/358 `/scratch/stefan/7774412/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC(C)C)N2C=CN=C2)S1) `REAL300004087282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087282 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC(C)C)N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 70, 70, 70, 46, 28, 26, 11, 26, 1, 11, 16, 16, 16, 1, 1, 1, 1, 1, 46, 46, 46, 46, 70, 70, 28, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1] 70 rigid atoms, others: [39, 40, 41, 12, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 293 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087282 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC(C)C)N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 18, 18, 18, 18, 18, 46, 46, 46, 46, 1, 2, 2, 2, 2, 2, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 46, 46, 46] 70 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 126 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087282 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087282/1 /scratch/stefan/7774412/working/building/REAL300004087282 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/359 `/scratch/stefan/7774412/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC(C)C)N2C=CN=C2)S1) `REAL300004087282.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087282/1/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: REAL300004087282 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC(C)C)N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 200, 201, 201, 157, 62, 24, 5, 24, 1, 5, 10, 10, 10, 1, 1, 1, 1, 1, 157, 157, 157, 157, 200, 200, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 12, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 528 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087282 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC(C)C)N2C=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 34, 34, 90, 95, 95, 95, 90, 157, 157, 157, 157, 1, 2, 2, 2, 2, 2, 90, 95, 95, 95, 95, 95, 95, 95, 95, 95, 157, 157, 157] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 507 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087282 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087282 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087282/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087282/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087282 Building REAL300004087283 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087283' /scratch/stefan/7774412/working/building/REAL300004087283 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087283 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087283/0 /scratch/stefan/7774412/working/building/REAL300004087283 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/360 `/scratch/stefan/7774412/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087283 none CCC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [35, 17, 17, 17, 17, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 35, 35, 35, 35, 35, 18, 18, 18, 17, 2, 2, 2, 2, 2, 2] 63 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087283 none CCC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 17, 17, 17, 32, 33, 33, 17, 17, 17, 5, 5, 5, 5, 5, 2, 2, 2, 1, 12, 32, 32, 18, 18, 18] 63 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087283 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087283 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087283/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087283 Building REAL300004087284 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087284' /scratch/stefan/7774412/working/building/REAL300004087284 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087284 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087284/0 /scratch/stefan/7774412/working/building/REAL300004087284 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/361 `/scratch/stefan/7774412/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCCCC3=C2)S1) `REAL300004087284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087284 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 16, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087284 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087284 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087284 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087284/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087284 Building REAL300004087285 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087285' /scratch/stefan/7774412/working/building/REAL300004087285 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087285 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087285/0 /scratch/stefan/7774412/working/building/REAL300004087285 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/362 `/scratch/stefan/7774412/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=CN=N3)C=CS2)S1) `REAL300004087285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087285 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=CN=N3)C=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 1] 6 rigid atoms, others: [32, 10, 12, 13, 14, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087285 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=CN=N3)C=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 4, 4, 4, 4, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 4, 4, 3, 3] 6 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087285 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(N3C=CN=N3)C=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 3, 4, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 6, 6, 4, 1, 1, 3, 3] 6 rigid atoms, others: [13, 14, 15, 16, 17, 18, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 20 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087285 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087285 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087285/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087285 Building REAL300004087286 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087286' /scratch/stefan/7774412/working/building/REAL300004087286 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087286 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087286/0 /scratch/stefan/7774412/working/building/REAL300004087286 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/363 `/scratch/stefan/7774412/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087286 none CCC(C)(C)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [54, 37, 5, 37, 37, 3, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 54, 54, 54, 54, 54, 37, 37, 37, 37, 37, 37, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 101 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087286 none CCC(C)(C)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 1, 4, 4, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 53, 53, 13, 13, 13, 1, 1, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 1, 1, 9, 25, 25, 13, 13, 13, 1, 1] 101 rigid atoms, others: [2, 35, 36, 5, 6, 7, 8, 9, 43, 44, 22, 23] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087286 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087286 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087286/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087286 Building REAL300004087287 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087287' /scratch/stefan/7774412/working/building/REAL300004087287 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087287 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087287/0 /scratch/stefan/7774412/working/building/REAL300004087287 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/364 `/scratch/stefan/7774412/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N1) `REAL300004087287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087287 none CC(=O)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [34, 17, 34, 17, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 34, 34, 34, 17, 17, 2, 2, 2, 2, 2, 2, 17] 57 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087287 none CC(=O)C1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 1, 1, 1, 1, 1, 11, 11, 13, 17, 17, 17, 29, 31, 31, 17, 17, 16, 1, 9, 9, 9, 1, 1, 13, 29, 29, 17, 17, 17, 1] 57 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 20, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087287 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087287 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087287/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087287 Building REAL300004087288 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087288' /scratch/stefan/7774412/working/building/REAL300004087288 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087288 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087288/0 /scratch/stefan/7774412/working/building/REAL300004087288 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/365 `/scratch/stefan/7774412/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1OC) `REAL300004087288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087288 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 13, 13, 13, 13, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 13, 21, 19, 19, 19, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 21, 21, 21] 33 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087288 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 23, 25, 25, 13, 13, 13, 1, 1, 1, 1, 5, 4, 4, 4, 1, 1, 13, 23, 23, 13, 13, 13, 2, 2, 2, 5, 5, 5] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087288 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087288 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087288/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087288 Building REAL300004087289 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087289' /scratch/stefan/7774412/working/building/REAL300004087289 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087289 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087289/0 /scratch/stefan/7774412/working/building/REAL300004087289 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/366 `/scratch/stefan/7774412/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087289 none COCCN1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 103, 63, 19, 19, 19, 19, 19, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 159, 159, 159, 103, 103, 63, 63, 19, 19, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 556 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087289 none COCCN1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 14, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 19, 19, 19, 37, 77, 77, 19, 19, 19, 44, 44, 44, 14, 14, 6, 6, 1, 1, 14, 37, 37, 19, 19, 19] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 379 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087289 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087289 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087289/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087289 Building REAL300004087290 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087290' /scratch/stefan/7774412/working/building/REAL300004087290 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087290 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087290/0 /scratch/stefan/7774412/working/building/REAL300004087290 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/367 `/scratch/stefan/7774412/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2=CC=CC(F)=C2)S1) `REAL300004087290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087290 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 51, 65, 65, 27, 16, 12, 1, 12, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 51, 51, 16, 1, 11, 11, 11, 11] 141 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087290 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 27, 27, 27, 27, 27, 81, 81, 81, 81, 81, 81, 1, 2, 2, 2, 2, 2, 2, 27, 81, 81, 81, 81] 141 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087290 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 8, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 141, 141, 141, 81, 55, 43, 11, 43, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 141, 141, 55, 11, 1, 1, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 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]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087290 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087290 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087290/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087290 Building REAL300004087291 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087291' /scratch/stefan/7774412/working/building/REAL300004087291 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087291 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087291/0 /scratch/stefan/7774412/working/building/REAL300004087291 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/368 `/scratch/stefan/7774412/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=NC=C3)N=C2)S1) `REAL300004087291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087291 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=NC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 22, 22, 22, 13, 9, 7, 1, 7, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 13, 13, 13, 13, 22, 22, 9, 1, 2, 2, 2, 2, 1] 22 rigid atoms, others: [35, 10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087291 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=NC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087291 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=CC=NC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 22, 22, 22, 13, 9, 7, 2, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 13, 13, 13, 13, 22, 22, 9, 2, 1, 1, 1, 1, 2] 22 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087291 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087291 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087291/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087291 Building REAL300004087292 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087292' /scratch/stefan/7774412/working/building/REAL300004087292 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087292 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087292/0 /scratch/stefan/7774412/working/building/REAL300004087292 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/369 `/scratch/stefan/7774412/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CC=C(Br)C=C2)S1) `REAL300004087292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087292 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CC=C(Br)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 99, 99, 99, 58, 43, 37, 9, 37, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 99, 99, 43, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1] 99 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 409 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087292 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CC=C(Br)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 53, 58, 58, 53, 55, 58, 58, 1, 2, 2, 2, 2, 2, 2, 22, 23, 23, 23, 53, 53, 58, 58, 58, 58] 99 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 277 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087292 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087292 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087292/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087292 Building REAL300004087293 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087293' /scratch/stefan/7774412/working/building/REAL300004087293 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087293 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087293/0 /scratch/stefan/7774412/working/building/REAL300004087293 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/370 `/scratch/stefan/7774412/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=C(Cl)S2)S1) `REAL300004087293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087293 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 32, 38, 38, 18, 16, 12, 1, 12, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 18, 19, 19, 19, 32, 32, 16, 1, 1, 12, 12] 71 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087293 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 49, 49, 49, 49, 49, 1, 2, 2, 2, 2, 2, 2, 18, 18, 49, 49] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087293 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 71, 71, 71, 49, 47, 39, 12, 39, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 71, 71, 47, 12, 12, 1, 1] 71 rigid atoms, others: [32, 33, 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]) total number of confs: 253 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087293 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087293 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087293/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087293 Building REAL300004087294 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087294' /scratch/stefan/7774412/working/building/REAL300004087294 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087294 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087294/0 /scratch/stefan/7774412/working/building/REAL300004087294 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/371 `/scratch/stefan/7774412/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=C(Cl)S2)S1) `REAL300004087294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087294 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 41, 57, 57, 21, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 21, 22, 22, 22, 41, 41, 14, 1, 2, 2, 2, 12, 12] 89 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 249 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087294 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 21, 21, 21, 21, 21, 21, 55, 55, 55, 55, 55, 1, 2, 2, 2, 2, 2, 2, 21, 22, 22, 22, 55, 55] 89 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087294 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 89, 89, 89, 55, 46, 43, 12, 43, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 89, 89, 46, 12, 12, 12, 12, 1, 1] 89 rigid atoms, others: [35, 36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087294 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087294 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087294/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087294 Building REAL300004087295 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087295' /scratch/stefan/7774412/working/building/REAL300004087295 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087295 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087295/0 /scratch/stefan/7774412/working/building/REAL300004087295 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/372 `/scratch/stefan/7774412/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2COC(C)(C)C)S1) `REAL300004087295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087295 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2COC(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 39, 55, 55, 19, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 19, 20, 20, 20, 38, 39, 12, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18] 100 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 281 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087295 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2COC(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 20, 3, 19, 19, 19, 54, 70, 70, 70, 70, 1, 2, 2, 2, 2, 2, 2, 20, 20, 3, 19, 54, 54, 70, 70, 70, 70, 70, 70, 70, 70, 70] 100 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 254 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087295 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087295 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087295/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087295 Building REAL300004087296 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087296' /scratch/stefan/7774412/working/building/REAL300004087296 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087296 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087296/0 /scratch/stefan/7774412/working/building/REAL300004087296 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/373 `/scratch/stefan/7774412/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C1=CN(C)N=C1) `REAL300004087296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087296 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 25, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 26, 26, 26, 26, 62, 62, 62, 62, 62, 26, 26, 26, 26, 2, 2, 2, 2, 2, 2, 26, 26, 26, 62, 62, 62, 62, 62] 100 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 125 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087296 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 17, 26, 26, 26, 49, 54, 54, 26, 26, 26, 1, 1, 1, 1, 8, 8, 8, 8, 8, 2, 2, 2, 1, 17, 49, 49, 26, 26, 26, 2, 2, 2, 8, 8, 8, 8, 8] 100 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 20, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 239 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087296 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)N1C1=CN(C)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 1, 8, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 47, 47, 48, 62, 62, 62, 100, 100, 100, 62, 62, 62, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 48, 100, 100, 62, 62, 62, 8, 8, 8, 1, 2, 2, 2, 1] 100 rigid atoms, others: [39, 43, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 363 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087296 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087296 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087296/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087296 Building REAL300004087297 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087297' /scratch/stefan/7774412/working/building/REAL300004087297 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087297 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087297/0 /scratch/stefan/7774412/working/building/REAL300004087297 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/374 `/scratch/stefan/7774412/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C2C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=CNC2=CC=C1) `REAL300004087297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087297 none CCOC1=C2C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=CNC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [68, 58, 33, 33, 33, 15, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 33, 33, 33, 33, 33, 33, 68, 68, 68, 68, 68, 15, 15, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33] 99 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 209 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: REAL300004087297 none CCOC1=C2C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=CNC2=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 5, 31, 31, 33, 33, 33, 33, 61, 77, 77, 33, 33, 33, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 5, 5, 33, 61, 61, 33, 33, 33, 1, 1, 1, 1, 1] 99 rigid atoms, others: [2, 3, 4, 5, 6, 39, 40, 41, 42, 43, 20, 21, 22, 23, 24, 25] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 374 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087297 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087297 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087297/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087297 Building REAL300004087298 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087298' /scratch/stefan/7774412/working/building/REAL300004087298 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087298 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087298/0 /scratch/stefan/7774412/working/building/REAL300004087298 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/375 `/scratch/stefan/7774412/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCOCC1) `REAL300004087298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087298 none CCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 3, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 17 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087298 none CCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 1, 2, 3, 36, 37, 19, 33, 39, 34, 16, 17, 18, 35, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087298 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087298/1 /scratch/stefan/7774412/working/building/REAL300004087298 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/376 `/scratch/stefan/7774412/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCOCC1) `REAL300004087298.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087298/1/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: REAL300004087298 none CCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 112, 61, 12, 61, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 112, 113, 113, 113, 112, 148, 148, 148, 148, 148, 2, 2, 1, 1, 1, 112, 112, 113, 113, 113, 113, 113, 112] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087298 none CCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 4, 4, 22, 112, 112, 112, 155, 188, 188, 112, 112, 112, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 155, 154, 113, 112, 112, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 34, 16, 17, 18, 19, 20, 38, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087298 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087298 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087298/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087298/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087298 Building REAL300004087299 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087299' /scratch/stefan/7774412/working/building/REAL300004087299 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087299 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087299/0 /scratch/stefan/7774412/working/building/REAL300004087299 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/377 `/scratch/stefan/7774412/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(Cl)C(N)=C2Cl)S1) `REAL300004087299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087299 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(Cl)C(N)=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 1, 1, 2, 2] 5 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087299 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(Cl)C(N)=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087299 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087299 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087299/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087299 Building REAL300004087300 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087300' /scratch/stefan/7774412/working/building/REAL300004087300 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087300 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087300/0 /scratch/stefan/7774412/working/building/REAL300004087300 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/378 `/scratch/stefan/7774412/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NOC2=NC(CC)=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C12) `REAL300004087300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087300 none CCCC1=NOC2=NC(CC)=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 8, 1, 5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 7, 7, 7, 7, 7, 7, 7, 7, 17, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 17, 17, 17, 17, 17, 13, 13, 17, 17, 17, 17, 17, 7, 2, 2, 2, 2, 2, 2] 47 rigid atoms, others: [15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087300 none CCCC1=NOC2=NC(CC)=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 8, 1, 5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 1, 1, 1, 5, 5, 7, 7, 7, 7, 13, 27, 27, 7, 7, 7, 1, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 1, 7, 13, 13, 7, 7, 7] 47 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 39, 26] set([0, 1, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087300 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087300 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087300/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087300 Building REAL300004087301 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087301' /scratch/stefan/7774412/working/building/REAL300004087301 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087301 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087301/0 /scratch/stefan/7774412/working/building/REAL300004087301 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/379 `/scratch/stefan/7774412/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC3)N=N2)S1) `REAL300004087301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087301 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 26, 48, 48, 17, 14, 13, 1, 13, 1, 1, 1, 1, 9, 34, 34, 1, 1, 17, 17, 17, 17, 26, 26, 14, 1, 9, 9, 34, 34, 34, 34, 34] 100 rigid atoms, others: [10, 12, 13, 14, 15, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087301 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 55, 76, 76, 17, 17, 1, 2, 2, 2, 2, 2, 2, 17, 55, 55, 76, 76, 76, 76, 76] 100 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 283 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087301 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 100, 100, 100, 76, 64, 64, 34, 64, 34, 34, 9, 1, 1, 1, 1, 34, 34, 76, 76, 76, 76, 100, 100, 64, 34, 9, 9, 1, 1, 1, 1, 1] 100 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 317 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087301 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087301 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087301/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087301 Building REAL300004087302 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087302' /scratch/stefan/7774412/working/building/REAL300004087302 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087302 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087302/0 /scratch/stefan/7774412/working/building/REAL300004087302 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/380 `/scratch/stefan/7774412/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=N1) `REAL300004087302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087302 none CCCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [54, 46, 16, 16, 16, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 16, 16, 54, 54, 54, 54, 54, 46, 46, 16, 2, 2, 2, 2, 2, 2] 82 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 222 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087302 none CCCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 1, 1, 1, 1, 1, 13, 13, 13, 16, 16, 16, 25, 44, 44, 16, 16, 16, 1, 1, 13, 13, 13, 13, 13, 9, 9, 1, 13, 25, 25, 16, 16, 16] 82 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087302 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087302 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087302/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087302 Building REAL300004087303 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087303' /scratch/stefan/7774412/working/building/REAL300004087303 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087303 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087303/0 /scratch/stefan/7774412/working/building/REAL300004087303 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/381 `/scratch/stefan/7774412/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C(C)C)N=N2)S1) `REAL300004087303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087303 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C(C)C)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 18, 31, 47, 47, 18, 12, 12, 1, 12, 1, 1, 1, 1, 13, 13, 1, 1, 17, 18, 18, 18, 31, 31, 12, 1, 13, 13, 13, 13, 13, 13, 13] 54 rigid atoms, others: [10, 12, 13, 14, 15, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087303 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C(C)C)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 38, 38, 17, 17, 1, 2, 2, 2, 2, 2, 2, 18, 38, 38, 38, 38, 38, 38, 38] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087303 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087303 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087303/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087303 Building REAL300004087304 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087304' /scratch/stefan/7774412/working/building/REAL300004087304 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087304 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087304/0 /scratch/stefan/7774412/working/building/REAL300004087304 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/382 `/scratch/stefan/7774412/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)=NO1) `REAL300004087304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087304 none CC1=NC(CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 9, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 16, 27, 27, 9, 9, 9, 1, 1, 43, 43, 43, 43, 43, 9, 9, 1, 6, 16, 16, 10, 10, 10] 179 rigid atoms, others: [4, 5, 6, 7, 8, 21, 22, 30] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) 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: REAL300004087304 none CC1=NC(CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 43, 43, 43, 94, 94, 94, 123, 123, 123, 179, 179, 179, 123, 123, 123, 43, 43, 1, 1, 2, 2, 2, 8, 8, 43, 94, 179, 179, 123, 123, 123] 179 rigid atoms, others: [0, 1, 2, 3, 4, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087304 none CC1=NC(CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 46, 9, 9, 9, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 9, 123, 123, 123, 123, 123, 46, 46, 9, 2, 2, 2, 2, 2, 2] 179 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 295 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087304 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087304 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087304/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087304 Building REAL300004087305 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087305' /scratch/stefan/7774412/working/building/REAL300004087305 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087305 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087305/0 /scratch/stefan/7774412/working/building/REAL300004087305 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/383 `/scratch/stefan/7774412/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CSC=C2)S1) `REAL300004087305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087305 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CSC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 41, 55, 55, 22, 17, 13, 1, 13, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 22, 22, 22, 41, 41, 17, 1, 1, 11, 11, 11] 102 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087305 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CSC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 22, 22, 67, 67, 67, 67, 1, 2, 2, 2, 2, 2, 2, 22, 22, 67, 67, 67] 102 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087305 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CSC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 102, 102, 102, 67, 57, 43, 11, 43, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 102, 102, 57, 11, 11, 1, 1, 1] 102 rigid atoms, others: [32, 33, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 378 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087305 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087305 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087305/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087305 Building REAL300004087306 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087306' /scratch/stefan/7774412/working/building/REAL300004087306 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087306 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087306/0 /scratch/stefan/7774412/working/building/REAL300004087306 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/384 `/scratch/stefan/7774412/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCOC3)N=N2)S1) `REAL300004087306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087306 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCOC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 9, 15, 33, 33, 9, 5, 5, 1, 5, 1, 1, 1, 1, 9, 31, 31, 31, 31, 1, 1, 8, 9, 9, 9, 15, 15, 6, 1, 9, 9, 31, 31, 31, 31, 31, 31, 31] 129 rigid atoms, others: [10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087306 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCOC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 49, 79, 79, 79, 79, 8, 8, 1, 2, 2, 2, 2, 2, 2, 9, 49, 49, 79, 79, 79, 79, 79, 79, 79] 129 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 304 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087306 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCOC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 12, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 129, 129, 129, 79, 55, 55, 31, 55, 31, 31, 7, 1, 1, 1, 1, 1, 1, 31, 31, 79, 79, 79, 79, 129, 129, 55, 31, 7, 7, 1, 1, 1, 1, 1, 1, 1] 129 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 473 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087306 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087306 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087306/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087306 Building REAL300004087307 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087307' /scratch/stefan/7774412/working/building/REAL300004087307 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087307 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087307/0 /scratch/stefan/7774412/working/building/REAL300004087307 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/385 `/scratch/stefan/7774412/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CN2N=NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2C)=NO1) `REAL300004087307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087307 none CC1=CC(CN2N=NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 9, 15, 15, 5, 5, 5, 1, 1, 21, 21, 21, 21, 21, 21, 7, 7, 5, 9, 9, 6, 6, 6, 2, 2, 2] 33 rigid atoms, others: [4, 5, 6, 7, 8, 9, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087307 none CC1=CC(CN2N=NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 21, 21, 21, 21, 29, 29, 29, 29, 29, 29, 33, 33, 33, 29, 29, 29, 21, 21, 1, 1, 2, 2, 2, 1, 8, 8, 29, 33, 33, 29, 29, 29, 21, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087307 none CC1=CC(CN2N=NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2C)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 17, 5, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 5, 6, 29, 29, 29, 29, 29, 29, 17, 16, 2, 2, 2, 2, 2, 2, 6, 6, 6] 33 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 106 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087307 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087307 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087307/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087307 Building REAL300004087308 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087308' /scratch/stefan/7774412/working/building/REAL300004087308 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087308 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087308/0 /scratch/stefan/7774412/working/building/REAL300004087308 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/386 `/scratch/stefan/7774412/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(CC3CCCC3)N=N2)S1) `REAL300004087308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087308 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(CC3CCCC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [8, 9, 9, 9, 17, 30, 30, 9, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 18, 18, 18, 18, 1, 1, 8, 9, 9, 9, 17, 17, 6, 2, 2, 2, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18] 83 rigid atoms, others: [10, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 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: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087308 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(CC3CCCC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 38, 53, 53, 53, 53, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 38, 38, 53, 53, 53, 53, 53, 53, 53, 53, 53] 83 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087308 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(CC3CCCC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 5, 5, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [53, 53, 53, 53, 83, 83, 83, 53, 38, 38, 18, 38, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 18, 18, 53, 53, 53, 53, 83, 83, 38, 18, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 83 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 307 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087308 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087308 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087308/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087308 Building REAL300004087309 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087309' /scratch/stefan/7774412/working/building/REAL300004087309 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087309 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087309/0 /scratch/stefan/7774412/working/building/REAL300004087309 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/387 `/scratch/stefan/7774412/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=N[N-]N=N3)C=N2)S1) `REAL300004087309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087309 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=N[N-]N=N3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 7, 13, 13, 13, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 12, 13, 5, 1, 1, 1] 13 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087309 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=N[N-]N=N3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087309 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=N[N-]N=N3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 13, 13, 13, 10, 9, 9, 2, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 10, 11, 11, 11, 12, 13, 9, 2, 2, 2] 13 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 45 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087309 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087309/1 /scratch/stefan/7774412/working/building/REAL300004087309 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/388 `/scratch/stefan/7774412/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NN=N[N-]3)C=N2)S1) `REAL300004087309.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087309 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NN=N[N-]3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 7, 13, 13, 13, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 13, 13, 5, 1, 1, 1] 13 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087309 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NN=N[N-]3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 7, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087309 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=NN=N[N-]3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 13, 13, 12, 10, 10, 2, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 12, 13, 13, 13, 12, 12, 10, 2, 2, 2] 13 rigid atoms, others: [15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 37 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087309 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087309 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087309/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087309/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087309 Building REAL300004087310 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087310' /scratch/stefan/7774412/working/building/REAL300004087310 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087310 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087310/0 /scratch/stefan/7774412/working/building/REAL300004087310 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/389 `/scratch/stefan/7774412/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CN(C)N=C2)S1) `REAL300004087310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087310 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 139, 139, 139, 85, 72, 63, 20, 63, 7, 18, 1, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 139, 139, 72, 20, 20, 20, 20, 7, 7, 1, 2, 2, 2, 1] 139 rigid atoms, others: [34, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37]) total number of confs: 599 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087310 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 44, 85, 85, 85, 85, 85, 1, 2, 2, 2, 2, 2, 2, 16, 17, 17, 17, 44, 44, 85, 85, 85, 85, 85] 139 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 282 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087310 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087310 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087310/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087310 Building REAL300004087311 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087311' /scratch/stefan/7774412/working/building/REAL300004087311 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087311 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087311/0 /scratch/stefan/7774412/working/building/REAL300004087311 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/390 `/scratch/stefan/7774412/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C(C2=CN(C)N=C2)O1) `REAL300004087311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087311 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C(C2=CN(C)N=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 1, 8, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 19, 19, 19, 40, 40, 40, 40, 39, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40] 55 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087311 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C(C2=CN(C)N=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 1, 8, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 14, 19, 19, 19, 35, 45, 45, 19, 18, 19, 1, 1, 1, 5, 5, 5, 5, 5, 1, 2, 2, 2, 14, 35, 35, 19, 19, 19, 5, 5, 5, 5, 5] 55 rigid atoms, others: [0, 1, 2, 3, 16, 17, 18, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087311 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C(C2=CN(C)N=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 1, 8, 5, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 24, 25, 33, 40, 40, 40, 55, 55, 55, 40, 40, 40, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 55, 55, 40, 40, 40, 1, 2, 2, 2, 1] 55 rigid atoms, others: [34, 38, 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, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087311 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087311 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087311/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087311 Building REAL300004087312 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087312' /scratch/stefan/7774412/working/building/REAL300004087312 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087312 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087312/0 /scratch/stefan/7774412/working/building/REAL300004087312 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/391 `/scratch/stefan/7774412/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3N=CC=C3N=C2C)S1) `REAL300004087312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087312 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3N=CC=C3N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 19, 19, 19, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 8, 1, 1, 1, 2, 2, 2] 19 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087312 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3N=CC=C3N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087312 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087312 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087312/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087312 Building REAL300004087313 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087313' /scratch/stefan/7774412/working/building/REAL300004087313 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087313 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087313/0 /scratch/stefan/7774412/working/building/REAL300004087313 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/392 `/scratch/stefan/7774412/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(OCC(F)F)=C2)S1) `REAL300004087313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087313 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(OCC(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 5, 7, 7, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 5, 5, 7, 1] 7 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087313 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(OCC(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 5, 5, 7, 7, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 7, 3] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087313 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087313 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087313/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087313 Building REAL300004087314 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087314' /scratch/stefan/7774412/working/building/REAL300004087314 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087314 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087314/0 /scratch/stefan/7774412/working/building/REAL300004087314 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/393 `/scratch/stefan/7774412/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC(C)C)N=C2C(F)F)S1) `REAL300004087314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087314 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC(C)C)N=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 5, 15, 15, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 41, 73, 73, 22, 12, 12, 1, 12, 1, 1, 1, 1, 5, 7, 7, 1, 1, 1, 10, 10, 22, 23, 23, 23, 40, 41, 12, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 10] 192 rigid atoms, others: [10, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 324 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087314 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC(C)C)N=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 5, 15, 15, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 74, 88, 88, 22, 22, 22, 52, 52, 1, 2, 2, 2, 2, 2, 2, 22, 74, 74, 88, 88, 88, 88, 88, 88, 88, 52] 192 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087314 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087314 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087314/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087314 Building REAL300004087315 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087315' /scratch/stefan/7774412/working/building/REAL300004087315 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087315 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087315/0 /scratch/stefan/7774412/working/building/REAL300004087315 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/394 `/scratch/stefan/7774412/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2OCC(F)F)S1) `REAL300004087315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087315 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2OCC(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 3, 3, 7] 7 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087315 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CN=C2OCC(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 5, 7, 7, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 5, 5, 7] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087315 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087315 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087315/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087315 Building REAL300004087316 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087316' /scratch/stefan/7774412/working/building/REAL300004087316 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087316 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087316/0 /scratch/stefan/7774412/working/building/REAL300004087316 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/395 `/scratch/stefan/7774412/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC(F)F)=N2)S1) `REAL300004087316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087316 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 14, 31, 31, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 24, 64, 64, 1, 8, 9, 9, 9, 14, 14, 5, 1, 1, 1, 24, 24, 64] 116 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087316 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 8, 8, 8, 8, 8, 21, 69, 96, 96, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 69, 69, 96] 116 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087316 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087316 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087316/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087316 Building REAL300004087317 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087317' /scratch/stefan/7774412/working/building/REAL300004087317 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087317 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087317/0 /scratch/stefan/7774412/working/building/REAL300004087317 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/396 `/scratch/stefan/7774412/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1C) `REAL300004087317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087317 none CC(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [21, 11, 21, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 11, 11, 11, 11, 21, 21, 21, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11] 39 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087317 none CC(=O)C1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 21, 21, 11, 11, 11, 1, 1, 1, 1, 3, 3, 3, 1, 7, 21, 21, 11, 11, 11, 1, 1, 2, 2, 2] 39 rigid atoms, others: [1, 34, 3, 4, 5, 6, 33, 19, 20, 21, 22, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087317 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087317 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087317/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087317 Building REAL300004087318 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087318' /scratch/stefan/7774412/working/building/REAL300004087318 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087318 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087318/0 /scratch/stefan/7774412/working/building/REAL300004087318 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/397 `/scratch/stefan/7774412/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=C(C)C=CN3C=N2)S1) `REAL300004087318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087318 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=C(C)C=CN3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 17, 29, 29, 29, 16, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 29, 29, 11, 1, 2, 2, 2, 1, 1, 1] 29 rigid atoms, others: [33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087318 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=C(C)C=CN3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 17, 17, 17, 17, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 16, 16] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087318 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087318 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087318/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087318 Building REAL300004087319 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087319' /scratch/stefan/7774412/working/building/REAL300004087319 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087319 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087319/0 /scratch/stefan/7774412/working/building/REAL300004087319 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/398 `/scratch/stefan/7774412/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CN=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087319 none CCC1=CC=CN=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 11, 11, 11, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 13, 13, 11, 11, 11, 2, 2, 2, 2, 2, 2] 23 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087319 none CCC1=CC=CN=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 11, 11, 11, 19, 19, 19, 11, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 9, 19, 19, 11, 11, 11] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 26, 27, 28] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087319 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087319 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087319/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087319 Building REAL300004087320 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087320' /scratch/stefan/7774412/working/building/REAL300004087320 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087320 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087320/0 /scratch/stefan/7774412/working/building/REAL300004087320 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/399 `/scratch/stefan/7774412/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1CCCCC1) `REAL300004087320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087320 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 18, 18, 18, 18, 18, 14, 14, 14, 13, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 25 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087320 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 22, 23, 23, 13, 13, 13, 1, 1, 1, 4, 4, 4, 4, 4, 2, 2, 2, 1, 10, 22, 22, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 25 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087320 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 15, 18, 18, 18, 25, 25, 25, 18, 18, 18, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 15, 25, 25, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 81 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087320 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087320 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087320/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087320 Building REAL300004087321 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087321' /scratch/stefan/7774412/working/building/REAL300004087321 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087321 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087321/0 /scratch/stefan/7774412/working/building/REAL300004087321 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/400 `/scratch/stefan/7774412/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C(C)C1CC1) `REAL300004087321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087321 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 5, 5, 5, 6, 5, 6, 6, 6, 6, 6, 5, 2, 2, 2, 2, 2, 2, 5, 6, 6, 6, 6, 6, 6, 6, 6] 11 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087321 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 6, 11, 11, 11, 5, 5, 5, 1, 1, 1, 2, 2, 3, 3, 2, 2, 2, 1, 3, 11, 11, 6, 6, 6, 2, 2, 2, 2, 3, 3, 3, 3, 3] 11 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087321 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C(C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 4, 6, 6, 6, 11, 11, 11, 6, 6, 6, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 3, 4, 11, 11, 6, 6, 6, 2, 2, 2, 2, 1, 1, 1, 1, 1] 11 rigid atoms, others: [38, 39, 40, 41, 42, 19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087321 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087321 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087321/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087321 Building REAL300004087322 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087322' /scratch/stefan/7774412/working/building/REAL300004087322 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087322 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087322/0 /scratch/stefan/7774412/working/building/REAL300004087322 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/401 `/scratch/stefan/7774412/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(CN(C)C)=C2)S1) `REAL300004087322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087322 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(CN(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 10, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 26, 45, 45, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 9, 24, 24, 1, 13, 14, 14, 14, 26, 26, 10, 8, 8, 24, 24, 24, 24, 24, 24, 1] 118 rigid atoms, others: [36, 10, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 252 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087322 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(CN(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 10, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 64, 87, 87, 13, 1, 2, 2, 2, 2, 2, 2, 63, 63, 87, 87, 87, 87, 87, 87, 13] 118 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087322 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087322/1 /scratch/stefan/7774412/working/building/REAL300004087322 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/402 `/scratch/stefan/7774412/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C[NH+](C)C)=C2)S1) `REAL300004087322.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087322/1/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: REAL300004087322 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C[NH+](C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 9, 6, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 10, 10, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 10, 10, 10, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 10, 10, 10, 10, 10, 10, 1] 10 rigid atoms, others: [37, 10, 12, 13, 14, 15, 16, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087322 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C[NH+](C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 9, 6, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 10, 10, 10, 10, 7, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 7] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087322 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087322 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087322/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087322/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087322 Building REAL300004087323 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087323' /scratch/stefan/7774412/working/building/REAL300004087323 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087323 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087323/0 /scratch/stefan/7774412/working/building/REAL300004087323 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/403 `/scratch/stefan/7774412/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N(C)C)N=CN=C3N2C)S1) `REAL300004087323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087323 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N(C)C)N=CN=C3N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 37, 42, 42, 21, 14, 12, 1, 12, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 37, 37, 14, 1, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2] 43 rigid atoms, others: [32, 39, 10, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 191 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087323 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N(C)C)N=CN=C3N2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 8, 1, 8, 1, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 21, 21, 21, 21, 41, 41, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 2, 2, 2, 21, 41, 41, 41, 41, 41, 41, 21, 21, 21, 21] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 129 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087323 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087323 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087323/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087323 Building REAL300004087324 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087324' /scratch/stefan/7774412/working/building/REAL300004087324 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087324 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087324/0 /scratch/stefan/7774412/working/building/REAL300004087324 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/404 `/scratch/stefan/7774412/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)N1N=C(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087324 none CCC(CC)N1N=C(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [33, 26, 17, 26, 33, 17, 17, 17, 17, 17, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 33, 33, 33, 33, 33, 26, 33, 33, 33, 33, 33, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2] 67 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 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: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087324 none CCC(CC)N1N=C(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 8, 1, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [7, 4, 1, 4, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 17, 17, 17, 33, 49, 49, 17, 17, 17, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 2, 2, 2, 1, 10, 33, 33, 17, 17, 17] 67 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087324 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087324 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087324/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087324 Building REAL300004087325 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087325' /scratch/stefan/7774412/working/building/REAL300004087325 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087325 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087325/0 /scratch/stefan/7774412/working/building/REAL300004087325 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/405 `/scratch/stefan/7774412/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(OCC(F)F)=CC=N2)S1) `REAL300004087325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087325 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(OCC(F)F)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 12, 12, 4, 3, 3, 1, 3, 1, 1, 1, 1, 6, 14, 29, 29, 1, 1, 1, 4, 5, 5, 5, 7, 7, 3, 1, 14, 14, 29, 1, 1] 41 rigid atoms, others: [34, 35, 10, 12, 13, 14, 15, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087325 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(OCC(F)F)=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 12, 5, 5, 15, 15, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 4, 4, 4, 16, 26, 39, 39, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 26, 26, 39, 4, 4] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087325 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087325 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087325/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087325 Building REAL300004087326 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087326' /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087326 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087326/0 /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/406 `/scratch/stefan/7774412/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1) `REAL300004087326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2] 5 rigid atoms, others: [33, 34, 35, 44, 10, 43, 12, 13, 14, 15, 16, 23, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 16 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087326/1 /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/407 `/scratch/stefan/7774412/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1) `REAL300004087326.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087326/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 2, 2, 3, 3, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 2] 13 rigid atoms, others: [33, 34, 35, 44, 10, 43, 12, 13, 14, 15, 16, 23, 24, 25, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 3, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 7, 7, 7, 3, 3, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087326/2 /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/408 `/scratch/stefan/7774412/working/3D/408' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1) `REAL300004087326.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087326/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 10, 8, 1, 8, 1, 1, 1, 1, 1, 6, 8, 8, 8, 8, 8, 1, 1, 1, 20, 20, 20, 20, 20, 20, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 1, 1, 1, 2, 2, 2] 32 rigid atoms, others: [32, 33, 34, 44, 10, 43, 12, 13, 14, 15, 16, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 10, 18, 18, 20, 20, 20, 20, 32, 32, 32, 32, 32, 32, 20, 20, 20, 1, 2, 2, 2, 2, 2, 20, 20, 20, 32, 32, 32, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 21, 18, 8, 18, 8, 8, 4, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 32, 32, 32, 32, 32, 32, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 32 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47]) total number of confs: 78 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087326/3 /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/409 `/scratch/stefan/7774412/working/3D/409' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1) `REAL300004087326.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087326/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 44, 10, 43, 12, 13, 14, 15, 16, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47]) total number of confs: 30 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 6, 6, 6, 1, 2, 2, 2, 2, 2, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 33 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087326 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2C[N@H+](CC3=CC=CC=C3)CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 4, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 19 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087326 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087326 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087326/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087326/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087326/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087326/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087326 Building REAL300004087327 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087327' /scratch/stefan/7774412/working/building/REAL300004087327 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087327 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087327/0 /scratch/stefan/7774412/working/building/REAL300004087327 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/410 `/scratch/stefan/7774412/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CN2N=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C12) `REAL300004087327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087327 none COC1=CC=CN2N=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 18, 18, 18, 18, 18, 18, 18, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 18, 22, 22, 22, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2] 39 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087327 none COC1=CC=CN2N=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 18, 18, 18, 35, 39, 39, 18, 18, 18, 1, 3, 3, 3, 1, 1, 1, 1, 14, 35, 35, 18, 18, 18] 39 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 27, 28, 29, 30] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087327 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087327 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087327/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087327 Building REAL300004087328 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087328' /scratch/stefan/7774412/working/building/REAL300004087328 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087328 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087328/0 /scratch/stefan/7774412/working/building/REAL300004087328 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/411 `/scratch/stefan/7774412/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCC3)N=C2)S1) `REAL300004087328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087328 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 21, 26, 26, 13, 9, 7, 1, 7, 1, 1, 1, 1, 11, 11, 11, 1, 1, 13, 13, 13, 13, 21, 21, 9, 1, 11, 11, 11, 11, 11, 11, 11, 1] 71 rigid atoms, others: [36, 10, 12, 13, 14, 15, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087328 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 53, 53, 53, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 53, 53, 53, 53, 53, 53, 53, 13] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087328 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 71, 71, 71, 53, 35, 35, 11, 35, 11, 11, 1, 1, 1, 1, 1, 11, 11, 53, 53, 53, 53, 71, 71, 35, 11, 1, 1, 1, 1, 1, 1, 1, 11] 71 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 222 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087328 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087328 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087328/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087328 Building REAL300004087329 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087329' /scratch/stefan/7774412/working/building/REAL300004087329 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087329 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087329/0 /scratch/stefan/7774412/working/building/REAL300004087329 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/412 `/scratch/stefan/7774412/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CC=C3O2)S1) `REAL300004087329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087329 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CC=C3O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 13, 23, 23, 23, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 23, 23, 9, 1, 1, 1, 1] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087329 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CC=C3O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 13, 13, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087329 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087329 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087329/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087329 Building REAL300004087330 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087330' /scratch/stefan/7774412/working/building/REAL300004087330 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087330 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087330/0 /scratch/stefan/7774412/working/building/REAL300004087330 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/413 `/scratch/stefan/7774412/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOC1=CC=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C) `REAL300004087330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087330 none COCCCOC1=CC=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 171, 95, 55, 15, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 187, 187, 187, 165, 165, 109, 109, 55, 55, 3, 3, 3, 2, 2, 2, 2, 2, 2, 3, 3, 3] 201 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 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: 899 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087330 none COCCCOC1=CC=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 119, 55, 31, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 11, 11, 3, 3, 3, 1, 1, 163, 163, 163, 111, 111, 67, 67, 31, 31, 1, 1, 1, 3, 5, 5, 3, 3, 3, 2, 2, 2] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 24, 25, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 697 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087330 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087330 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087330/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087330 Building REAL300004087331 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087331' /scratch/stefan/7774412/working/building/REAL300004087331 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087331 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087331/0 /scratch/stefan/7774412/working/building/REAL300004087331 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/414 `/scratch/stefan/7774412/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1C(F)(F)F) `REAL300004087331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087331 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 1, 5, 12, 12, 13, 21, 21, 21, 40, 40, 40, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 5, 13, 40, 40, 21, 21, 21, 1, 1, 1, 1] 40 rigid atoms, others: [2, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087331 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 21, 21, 15, 21, 21, 21, 21, 21, 21, 16, 16, 16, 14, 2, 2, 2, 2, 2, 2, 21, 21, 17, 21] 40 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087331 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087331/1 /scratch/stefan/7774412/working/building/REAL300004087331 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/415 `/scratch/stefan/7774412/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1C(F)(F)F) `REAL300004087331.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087331/1/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: REAL300004087331 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 3, 5, 5, 29, 108, 108, 108, 162, 162, 162, 108, 108, 108, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 3, 162, 162, 108, 108, 108, 1, 1, 1, 1] 162 rigid atoms, others: [2, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 482 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087331 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [109, 93, 76, 12, 76, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 93, 108, 108, 93, 108, 108, 108, 108, 108, 108, 109, 109, 109, 93, 3, 3, 2, 2, 2, 108, 108, 93, 108] 162 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087331 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087331 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087331/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087331/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087331 Building REAL300004087332 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087332' /scratch/stefan/7774412/working/building/REAL300004087332 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087332 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087332/0 /scratch/stefan/7774412/working/building/REAL300004087332 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/416 `/scratch/stefan/7774412/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C2CCC2)S1) `REAL300004087332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087332 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 42, 58, 58, 23, 16, 12, 1, 12, 1, 1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 23, 42, 42, 16, 1, 1, 8, 8, 8, 8, 8, 8, 8] 77 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 249 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: REAL300004087332 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 23, 23, 23, 23, 23, 53, 53, 53, 1, 2, 2, 2, 2, 2, 2, 23, 23, 53, 53, 53, 53, 53, 53, 53] 77 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087332 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 77, 77, 77, 53, 42, 35, 8, 35, 8, 8, 8, 8, 1, 1, 1, 1, 1, 53, 53, 53, 53, 77, 77, 42, 8, 8, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 269 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087332 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087332 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087332/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087332 Building REAL300004087333 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087333' /scratch/stefan/7774412/working/building/REAL300004087333 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087333 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087333/0 /scratch/stefan/7774412/working/building/REAL300004087333 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/417 `/scratch/stefan/7774412/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC=N1) `REAL300004087333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087333 none CC1=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 27, 27, 27, 27, 27, 27, 12, 12, 2, 2, 2, 2, 2, 2, 27] 43 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087333 none CC1=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 25, 25, 25, 27, 27, 27, 43, 43, 43, 27, 27, 27, 1, 1, 1, 2, 2, 2, 9, 9, 25, 43, 43, 27, 27, 27, 1] 43 rigid atoms, others: [0, 1, 2, 3, 32, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087333 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087333 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087333/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087333 Building REAL300004087334 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087334' /scratch/stefan/7774412/working/building/REAL300004087334 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087334 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087334/0 /scratch/stefan/7774412/working/building/REAL300004087334 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/418 `/scratch/stefan/7774412/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(Cl)C=C2)S1) `REAL300004087334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087334 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 11, 11, 7, 7, 7, 3, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 3, 3, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087334 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 7, 7, 5, 5, 7, 7, 1, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7, 7] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087334 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087334 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087334/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087334 Building REAL300004087335 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087335' /scratch/stefan/7774412/working/building/REAL300004087335 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087335 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087335/0 /scratch/stefan/7774412/working/building/REAL300004087335 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/419 `/scratch/stefan/7774412/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2OCC3)S1) `REAL300004087335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087335 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2OCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 14, 14, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 7, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087335 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2OCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087335 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087335 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087335/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087335 Building REAL300004087336 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087336' /scratch/stefan/7774412/working/building/REAL300004087336 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087336 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087336/0 /scratch/stefan/7774412/working/building/REAL300004087336 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/420 `/scratch/stefan/7774412/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C(C(C)(C)C)O1) `REAL300004087336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087336 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C(C(C)(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 18, 18, 18, 29, 29, 29, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29] 46 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 119 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: REAL300004087336 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C(C(C)(C)C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 11, 11, 13, 18, 18, 18, 28, 31, 31, 18, 18, 18, 1, 1, 1, 4, 4, 4, 1, 2, 2, 2, 13, 28, 28, 18, 18, 18, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 46 rigid atoms, others: [0, 1, 2, 3, 32, 16, 17, 18, 22] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087336 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087336 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087336/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087336 Building REAL300004087337 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087337' /scratch/stefan/7774412/working/building/REAL300004087337 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087337 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087337/0 /scratch/stefan/7774412/working/building/REAL300004087337 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/421 `/scratch/stefan/7774412/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NO1) `REAL300004087337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087337 none CC1=CC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 10, 10, 10, 10, 10, 10, 4, 4, 2, 2, 2, 3, 3, 2, 2, 2] 16 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087337 none CC1=CC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 10, 10, 10, 1, 1, 2, 2, 2, 1, 7, 7, 10, 10, 10, 16, 16, 10, 10, 10] 16 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087337 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087337 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087337/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087337 Building REAL300004087338 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087338' /scratch/stefan/7774412/working/building/REAL300004087338 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087338 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087338/0 /scratch/stefan/7774412/working/building/REAL300004087338 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/422 `/scratch/stefan/7774412/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=C(C(C)(C)C)S2)S1) `REAL300004087338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087338 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=C(C(C)(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 57, 70, 70, 37, 37, 36, 11, 36, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 37, 37, 37, 37, 57, 57, 37, 11, 11, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 78 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 294 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087338 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=C(C(C)(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 12, 12, 37, 37, 37, 37, 55, 55, 55, 37, 1, 2, 2, 2, 3, 3, 2, 12, 12, 37, 55, 55, 55, 55, 55, 55, 55, 55, 55] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087338 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087338 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087338/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087338 Building REAL300004087339 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087339' /scratch/stefan/7774412/working/building/REAL300004087339 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087339 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087339/0 /scratch/stefan/7774412/working/building/REAL300004087339 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/423 `/scratch/stefan/7774412/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(NS(C)(=O)=O)C=C2)S1) `REAL300004087339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087339 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(NS(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 13, 13, 5, 5, 5, 3, 5, 3, 1, 1, 1, 1, 1, 1, 9, 13, 13, 13, 1, 1, 5, 5, 5, 5, 9, 9, 5, 3, 3, 1, 1, 9, 13, 13, 13, 1, 1] 25 rigid atoms, others: [34, 35, 40, 41, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087339 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(NS(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 5, 5, 3, 5, 19, 23, 23, 23, 5, 5, 1, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 19, 23, 23, 23, 5, 5] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087339 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087339 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087339/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087339 Building REAL300004087340 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087340' /scratch/stefan/7774412/working/building/REAL300004087340 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087340 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087340/0 /scratch/stefan/7774412/working/building/REAL300004087340 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/424 `/scratch/stefan/7774412/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OC1=CC=CC=C1C=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087340 none CCC(C)OC1=CC=CC=C1C=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 147, 111, 147, 36, 36, 36, 10, 36, 36, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 164, 164, 164, 164, 164, 147, 147, 147, 147, 36, 36, 36, 36, 8, 8, 2, 3, 3, 2, 2, 2] 201 rigid atoms, others: [15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 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: 553 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087340 none CCC(C)OC1=CC=CC=C1C=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 9, 20, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 36, 36, 36, 36, 36, 36, 59, 92, 92, 36, 36, 36, 35, 35, 35, 35, 35, 20, 20, 20, 20, 1, 1, 1, 1, 10, 10, 36, 59, 59, 36, 36, 36] 201 rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 11, 36, 38, 37] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 490 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087340 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087340 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087340/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087340 Building REAL300004087341 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087341' /scratch/stefan/7774412/working/building/REAL300004087341 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087341 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087341/0 /scratch/stefan/7774412/working/building/REAL300004087341 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/425 `/scratch/stefan/7774412/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC3=CC(Cl)=CC=C3C=C2)S1) `REAL300004087341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087341 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC3=CC(Cl)=CC=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 53, 53, 53, 34, 33, 33, 12, 32, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 53, 53, 33, 12, 12, 1, 1, 1, 1, 1] 53 rigid atoms, others: [34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087341 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC3=CC(Cl)=CC=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 16, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 33, 33, 34, 34, 1, 2, 2, 2, 2, 2, 2, 14, 14, 34, 34, 34, 34, 34] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087341 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087341 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087341/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087341 Building REAL300004087342 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087342' /scratch/stefan/7774412/working/building/REAL300004087342 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087342 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087342/0 /scratch/stefan/7774412/working/building/REAL300004087342 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/426 `/scratch/stefan/7774412/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC=C2CC2=CC=CC=C2)S1) `REAL300004087342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087342 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC=C2CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 39, 69, 69, 22, 17, 13, 1, 12, 1, 1, 1, 1, 1, 1, 10, 16, 16, 12, 16, 16, 21, 22, 22, 22, 39, 39, 17, 1, 1, 1, 10, 10, 16, 16, 16, 16, 16] 201 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 330 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087342 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC=C2CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 21, 21, 21, 22, 112, 116, 116, 116, 116, 116, 1, 2, 2, 2, 2, 2, 2, 22, 22, 22, 112, 112, 116, 116, 116, 116, 116] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 396 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087342 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC=C2CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 201, 201, 201, 116, 101, 87, 16, 87, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 201, 201, 101, 16, 16, 16, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 793 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087342 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087342 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087342/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087342 Building REAL300004087343 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087343' /scratch/stefan/7774412/working/building/REAL300004087343 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087343 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087343/0 /scratch/stefan/7774412/working/building/REAL300004087343 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/427 `/scratch/stefan/7774412/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C(C)C)S1) `REAL300004087343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087343 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 6, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 11 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 49 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087343 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 10, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087343 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087343 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087343/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087343 Building REAL300004087344 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087344' /scratch/stefan/7774412/working/building/REAL300004087344 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087344 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087344/0 /scratch/stefan/7774412/working/building/REAL300004087344 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/428 `/scratch/stefan/7774412/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC(C3CC3)=C2)S1) `REAL300004087344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087344 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 44, 79, 79, 23, 14, 12, 1, 12, 1, 1, 1, 8, 8, 1, 1, 1, 12, 12, 1, 23, 24, 24, 24, 43, 44, 15, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 1] 201 rigid atoms, others: [40, 10, 12, 13, 14, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087344 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 23, 23, 69, 69, 23, 23, 24, 102, 102, 24, 1, 2, 2, 2, 2, 2, 2, 69, 69, 69, 69, 69, 102, 102, 102, 102, 102, 24] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 382 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087344 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 152, 172, 172, 102, 78, 76, 12, 76, 12, 12, 12, 55, 55, 12, 1, 1, 1, 1, 12, 102, 102, 102, 102, 152, 152, 78, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 12] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 707 number of broken/clashed sets: 4 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087344 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 117, 153, 153, 68, 50, 48, 8, 48, 8, 1, 1, 1, 1, 8, 8, 8, 55, 55, 7, 68, 68, 68, 68, 117, 117, 50, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 8] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 696 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087344 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087344 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087344/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087344 Building REAL300004087345 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087345' /scratch/stefan/7774412/working/building/REAL300004087345 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087345 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087345/0 /scratch/stefan/7774412/working/building/REAL300004087345 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/429 `/scratch/stefan/7774412/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=CC=C2C)S1) `REAL300004087345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087345 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 44, 44, 44, 25, 19, 19, 5, 19, 1, 5, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 44, 44, 19, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2] 44 rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087345 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 20, 25, 25, 20, 25, 25, 25, 1, 2, 2, 2, 2, 2, 2, 20, 21, 21, 21, 25, 25, 20, 25, 25, 25, 25] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087345 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087345/1 /scratch/stefan/7774412/working/building/REAL300004087345 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/430 `/scratch/stefan/7774412/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=CC=C2C)S1) `REAL300004087345.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087345/1/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: REAL300004087345 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 201, 201, 201, 144, 61, 15, 4, 15, 1, 4, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 568 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087345 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 59, 59, 133, 133, 144, 144, 133, 144, 144, 144, 1, 2, 2, 2, 2, 2, 133, 133, 133, 133, 144, 144, 133, 144, 144, 144, 144] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 554 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087345 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087345 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087345/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087345/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087345 Building REAL300004087346 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087346' /scratch/stefan/7774412/working/building/REAL300004087346 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087346 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087346/0 /scratch/stefan/7774412/working/building/REAL300004087346 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/431 `/scratch/stefan/7774412/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087346 none COC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 16, 16, 16, 16, 16, 16, 15, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087346 none COC1=NN(C)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 15, 15, 15, 26, 27, 27, 15, 15, 15, 2, 2, 2, 2, 2, 2, 1, 12, 26, 26, 16, 16, 16] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087346 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087346 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087346/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087346 Building REAL300004087347 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087347' /scratch/stefan/7774412/working/building/REAL300004087347 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087347 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087347/0 /scratch/stefan/7774412/working/building/REAL300004087347 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/432 `/scratch/stefan/7774412/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(OC3CCCC3)=C2)S1) `REAL300004087347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087347 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(OC3CCCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 32, 56, 56, 20, 20, 20, 7, 20, 7, 1, 1, 1, 1, 1, 1, 1, 12, 34, 34, 34, 34, 1, 20, 20, 20, 20, 32, 32, 20, 7, 7, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1] 160 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 291 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087347 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(OC3CCCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 6, 20, 20, 20, 20, 20, 95, 134, 134, 134, 134, 20, 1, 2, 2, 2, 2, 2, 2, 6, 6, 20, 20, 20, 134, 134, 134, 134, 134, 134, 134, 134, 134, 20] 160 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 299 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087347 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(OC3CCCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 160, 160, 160, 134, 134, 134, 80, 134, 80, 34, 34, 34, 34, 34, 6, 1, 1, 1, 1, 1, 1, 34, 134, 134, 134, 134, 160, 160, 134, 80, 80, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34] 160 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 512 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087347 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087347 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087347/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087347 Building REAL300004087348 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087348' /scratch/stefan/7774412/working/building/REAL300004087348 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087348 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087348/0 /scratch/stefan/7774412/working/building/REAL300004087348 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/433 `/scratch/stefan/7774412/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(Br)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087348 none CCC1=CC=C(Br)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 8, 8, 4, 8, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 14, 14, 14, 14, 14, 8, 7, 8, 2, 2, 2, 2, 2, 2] 20 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087348 none CCC1=CC=C(Br)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 17, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 5, 5, 5, 5, 5, 1, 1, 1, 8, 14, 14, 8, 8, 8] 20 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087348 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087348 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087348/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087348 Building REAL300004087349 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087349' /scratch/stefan/7774412/working/building/REAL300004087349 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087349 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087349/0 /scratch/stefan/7774412/working/building/REAL300004087349 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/434 `/scratch/stefan/7774412/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(Br)=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087349 none COC1=CC(Br)=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 25, 25, 25, 13, 13, 2, 2, 2, 2, 2, 2, 13] 49 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087349 none COC1=CC(Br)=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 17, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 29, 29, 13, 13, 13, 1, 2, 2, 2, 1, 1, 9, 25, 25, 13, 13, 13, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 33, 21, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087349 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087349 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087349/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087349 Building REAL300004087350 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087350' /scratch/stefan/7774412/working/building/REAL300004087350 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087350 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087350/0 /scratch/stefan/7774412/working/building/REAL300004087350 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/435 `/scratch/stefan/7774412/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(OCC[NH+](C)C)C=C2)S1) `REAL300004087350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087350 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(OCC[NH+](C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 9, 6, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 16, 26, 26, 12, 12, 12, 3, 12, 3, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 1, 1, 12, 12, 12, 12, 16, 16, 12, 3, 3, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 40 rigid atoms, others: [48, 36, 37, 49, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 134 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087350 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(OCC[NH+](C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 9, 6, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 7, 12, 12, 7, 12, 22, 32, 32, 32, 32, 32, 12, 12, 1, 2, 2, 2, 2, 2, 2, 7, 7, 12, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 12, 12] 40 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 152 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087350 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087350 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087350/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087350 Building REAL300004087351 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087351' /scratch/stefan/7774412/working/building/REAL300004087351 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087351 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087351/0 /scratch/stefan/7774412/working/building/REAL300004087351 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/436 `/scratch/stefan/7774412/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NC=N1) `REAL300004087351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087351 none COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 8, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 8, 8, 8, 13, 13, 13, 8, 2, 2, 2, 2, 2, 2, 8] 23 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087351 none COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 7, 7, 7, 8, 8, 8, 16, 19, 19, 8, 8, 8, 1, 1, 1, 3, 3, 3, 1, 7, 16, 16, 9, 9, 9, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 24, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087351 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087351 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087351/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087351 Building REAL300004087352 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087352' /scratch/stefan/7774412/working/building/REAL300004087352 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087352 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087352/0 /scratch/stefan/7774412/working/building/REAL300004087352 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/437 `/scratch/stefan/7774412/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087352 none COC1=NC=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 12, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 19, 19, 19, 12, 12, 2, 2, 2, 2, 2, 2] 33 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087352 none COC1=NC=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 12, 12, 12, 20, 25, 25, 12, 12, 12, 1, 3, 3, 3, 1, 1, 11, 20, 20, 13, 13, 13] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 24, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087352 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087352 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087352/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087352 Building REAL300004087353 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087353' /scratch/stefan/7774412/working/building/REAL300004087353 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087353 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087353/0 /scratch/stefan/7774412/working/building/REAL300004087353 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/438 `/scratch/stefan/7774412/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(Br)=CC=CN3N=C2)S1) `REAL300004087353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087353 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(Br)=CC=CN3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 1, 1, 1, 1] 9 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087353 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(Br)=CC=CN3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087353 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087353 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087353/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087353 Building REAL300004087354 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087354' /scratch/stefan/7774412/working/building/REAL300004087354 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087354 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087354/0 /scratch/stefan/7774412/working/building/REAL300004087354 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/439 `/scratch/stefan/7774412/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(F)(F)F)O2)S1) `REAL300004087354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087354 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(F)(F)F)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 13, 13, 23, 23, 23, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 2, 2, 2, 1, 12, 13, 13, 13, 23, 23, 8, 1, 1] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087354 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(F)(F)F)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 15, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 13, 13, 13, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087354 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087354 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087354/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087354 Building REAL300004087355 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087355' /scratch/stefan/7774412/working/building/REAL300004087355 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087355 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087355/0 /scratch/stefan/7774412/working/building/REAL300004087355 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/440 `/scratch/stefan/7774412/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)C(C)(C)C2(C)C)S1) `REAL300004087355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087355 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)C(C)(C)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 14, 14, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 14 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 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: 83 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087355 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)C(C)(C)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 43 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087355 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087355/1 /scratch/stefan/7774412/working/building/REAL300004087355 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/441 `/scratch/stefan/7774412/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)C(C)(C)C2(C)C)S1) `REAL300004087355.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087355/1/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: REAL300004087355 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)C(C)(C)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 201, 201, 201, 145, 33, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145, 201, 201, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 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: 548 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087355 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)C(C)(C)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 79, 79, 145, 145, 145, 145, 145, 145, 145, 1, 2, 2, 2, 2, 2, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145, 145] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 433 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087355 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087355 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087355/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087355/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087355 Building REAL300004087356 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087356' /scratch/stefan/7774412/working/building/REAL300004087356 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087356 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087356/0 /scratch/stefan/7774412/working/building/REAL300004087356 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/442 `/scratch/stefan/7774412/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(COCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087356 none CCC1=NOC(COCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 86, 86, 86, 86, 42, 17, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 86, 146, 146, 146, 146, 146, 42, 42, 6, 6, 1, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 585 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087356 none CCC1=NOC(COCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 8, 33, 56, 86, 86, 86, 86, 86, 86, 118, 131, 131, 86, 86, 86, 1, 7, 7, 7, 7, 7, 8, 8, 56, 56, 86, 118, 118, 86, 86, 86] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087356 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087356/1 /scratch/stefan/7774412/working/building/REAL300004087356 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/443 `/scratch/stefan/7774412/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(COCC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087356.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087356/1/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: REAL300004087356 none CCC1=NOC(COCC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 108, 108, 108, 108, 76, 52, 46, 22, 8, 22, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 108, 182, 182, 182, 182, 182, 76, 76, 46, 46, 2, 2, 2, 2, 2] 201 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 837 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087356 none CCC1=NOC(COCC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 5, 13, 22, 30, 30, 68, 108, 108, 108, 125, 137, 137, 108, 108, 108, 1, 5, 5, 5, 5, 5, 5, 5, 22, 22, 125, 125, 108, 108, 108] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 22] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 406 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087356 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087356 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087356/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087356/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087356 Building REAL300004087357 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087357' /scratch/stefan/7774412/working/building/REAL300004087357 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087357 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087357/0 /scratch/stefan/7774412/working/building/REAL300004087357 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/444 `/scratch/stefan/7774412/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC2=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C(C)N=C2C=C1) `REAL300004087357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087357 none COC1=CC2=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C(C)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 15, 15, 15, 15, 25, 25, 25, 15, 15, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15] 31 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 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: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087357 none COC1=CC2=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C(C)N=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 15, 15, 15, 27, 31, 31, 15, 15, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 11, 27, 27, 15, 15, 15, 2, 2, 2, 1, 1] 31 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 41, 20, 21, 22, 23, 24, 25, 29, 30] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087357 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087357 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087357/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087357 Building REAL300004087358 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087358' /scratch/stefan/7774412/working/building/REAL300004087358 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087358 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087358/0 /scratch/stefan/7774412/working/building/REAL300004087358 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/445 `/scratch/stefan/7774412/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2=CC=CC=C2C)S1) `REAL300004087358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087358 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 18, 24, 24, 10, 10, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 10, 10, 10, 10, 18, 18, 10, 1, 1, 1, 1, 5, 5, 2, 5, 5, 5, 5] 32 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087358 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 18, 18, 10, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 18, 18, 18, 18, 18, 18, 18] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087358 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 32, 32, 32, 18, 18, 15, 5, 15, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 32, 32, 18, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2] 32 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087358 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087358 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087358/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087358 Building REAL300004087359 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087359' /scratch/stefan/7774412/working/building/REAL300004087359 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087359 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087359/0 /scratch/stefan/7774412/working/building/REAL300004087359 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/446 `/scratch/stefan/7774412/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC(C)=CC3=CC=C2C)S1) `REAL300004087359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087359 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC(C)=CC3=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 9, 9, 9, 17, 17, 17, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 39, 40, 41]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087359 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC(C)=CC3=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 8, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 8, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087359 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087359 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087359/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087359 Building REAL300004087360 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087360' /scratch/stefan/7774412/working/building/REAL300004087360 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087360 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087360/0 /scratch/stefan/7774412/working/building/REAL300004087360 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/447 `/scratch/stefan/7774412/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C=C2OC(F)(F)F)S1) `REAL300004087360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087360 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C=C2OC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 32, 55, 55, 18, 16, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 18, 19, 19, 19, 32, 32, 16, 1, 1, 2, 2, 2, 1] 83 rigid atoms, others: [32, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087360 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C=C2OC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 12, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 5, 18, 18, 18, 18, 51, 53, 53, 53, 1, 2, 2, 2, 2, 2, 2, 18, 18, 19, 19, 19, 18] 83 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087360 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087360 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087360/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087360 Building REAL300004087361 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087361' /scratch/stefan/7774412/working/building/REAL300004087361 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087361 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087361/0 /scratch/stefan/7774412/working/building/REAL300004087361 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/448 `/scratch/stefan/7774412/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=C(C)C=C2C)S1) `REAL300004087361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087361 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=C(C)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 17, 17, 17, 10, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 1, 2, 2, 2, 1, 2, 2, 2] 17 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087361 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=C(C)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087361 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087361 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087361/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087361 Building REAL300004087362 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087362' /scratch/stefan/7774412/working/building/REAL300004087362 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087362 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087362/0 /scratch/stefan/7774412/working/building/REAL300004087362 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/449 `/scratch/stefan/7774412/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CO3)=C2)S1) `REAL300004087362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087362 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CO3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 26, 26, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 11, 11, 11, 1] 57 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087362 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CO3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 43, 43, 43, 43, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 43, 43, 43, 13] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087362 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CO3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 57, 57, 57, 43, 35, 33, 11, 33, 11, 10, 11, 11, 1, 1, 1, 1, 1, 1, 11, 43, 43, 43, 43, 57, 57, 35, 10, 11, 1, 1, 1, 11] 57 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 183 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087362 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087362 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087362/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087362 Building REAL300004087363 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087363' /scratch/stefan/7774412/working/building/REAL300004087363 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087363 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087363/0 /scratch/stefan/7774412/working/building/REAL300004087363 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/450 `/scratch/stefan/7774412/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC(C(F)(F)F)=N2)S1) `REAL300004087363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087363 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC(C(F)(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 11, 11, 11, 19, 19, 10, 1, 1] 19 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087363 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC(C(F)(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 15, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 11, 11, 10, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 10] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087363 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087363 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087363/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087363 Building REAL300004087364 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087364' /scratch/stefan/7774412/working/building/REAL300004087364 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087364 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087364/0 /scratch/stefan/7774412/working/building/REAL300004087364 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/451 `/scratch/stefan/7774412/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=NC2=CC=CC=C2C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087364 none CCCOC1=NC2=CC=CC=C2C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [121, 112, 53, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 121, 121, 121, 121, 121, 112, 112, 20, 19, 20, 20, 20, 2, 2, 2, 2, 2, 2] 175 rigid atoms, others: [16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 432 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087364 none CCCOC1=NC2=CC=CC=C2C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [49, 37, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 20, 20, 20, 37, 61, 61, 19, 19, 19, 53, 53, 53, 53, 53, 37, 37, 1, 1, 1, 1, 1, 15, 37, 37, 20, 20, 20] 175 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 35, 36, 38, 37] set([0, 1, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087364 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087364 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087364/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087364 Building REAL300004087365 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087365' /scratch/stefan/7774412/working/building/REAL300004087365 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087365 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087365/0 /scratch/stefan/7774412/working/building/REAL300004087365 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/452 `/scratch/stefan/7774412/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=N3)=N2)S1) `REAL300004087365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087365 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 26, 40, 40, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 14, 15, 15, 15, 26, 26, 11, 1, 1, 13, 13, 12, 13] 74 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087365 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 48, 48, 48, 48, 48, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 48, 48, 48, 48] 74 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087365 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 74, 74, 74, 48, 34, 34, 13, 34, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 48, 48, 48, 48, 74, 74, 34, 12, 13, 1, 1, 1, 1] 74 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 259 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087365 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087365 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087365/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087365 Building REAL300004087366 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087366' /scratch/stefan/7774412/working/building/REAL300004087366 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087366 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087366/0 /scratch/stefan/7774412/working/building/REAL300004087366 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/453 `/scratch/stefan/7774412/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=CC=N2)S1) `REAL300004087366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087366 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 17, 25, 25, 25, 16, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 24, 25, 11, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087366 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=COC3=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 17, 17, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 17, 17, 16, 17] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087366 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087366 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087366/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087366 Building REAL300004087367 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087367' /scratch/stefan/7774412/working/building/REAL300004087367 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087367 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087367/0 /scratch/stefan/7774412/working/building/REAL300004087367 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/454 `/scratch/stefan/7774412/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCOC2CCCC3)S1) `REAL300004087367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087367 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCOC2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087367 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCOC2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087367 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087367/1 /scratch/stefan/7774412/working/building/REAL300004087367 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/455 `/scratch/stefan/7774412/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCOC2CCCC3)S1) `REAL300004087367.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087367/1/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: REAL300004087367 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCOC2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 135, 135, 135, 99, 24, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 135, 135, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087367 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCOC2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 60, 60, 99, 99, 99, 99, 99, 99, 99, 99, 1, 2, 2, 2, 2, 2, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 135 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087367 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087367 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087367/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087367/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087367 Building REAL300004087368 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087368' /scratch/stefan/7774412/working/building/REAL300004087368 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087368 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087368/0 /scratch/stefan/7774412/working/building/REAL300004087368 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/456 `/scratch/stefan/7774412/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1) `REAL300004087368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087368 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 21, 33, 33, 12, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 12, 12, 12, 12, 12, 1, 12, 12, 12, 12, 21, 21, 7, 1, 1, 1, 1, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12] 56 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087368 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 33, 37, 37, 37, 37, 37, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 33, 33, 37, 37, 37, 37, 37, 37, 37, 37] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087368 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 56, 56, 56, 37, 28, 26, 12, 26, 12, 12, 12, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 37, 56, 56, 28, 12, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 56 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 216 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087368 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087368/1 /scratch/stefan/7774412/working/building/REAL300004087368 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/457 `/scratch/stefan/7774412/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1) `REAL300004087368.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087368 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 126, 143, 143, 86, 30, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 1, 86, 86, 86, 86, 126, 126, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 452 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087368 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 44, 44, 86, 86, 86, 86, 86, 86, 143, 169, 169, 169, 169, 169, 86, 1, 2, 2, 2, 2, 2, 86, 86, 86, 86, 143, 143, 169, 169, 169, 169, 169, 169, 169, 169] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 605 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087368 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CC[C@H](CN3CCOCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 201, 201, 201, 169, 91, 38, 11, 38, 11, 11, 11, 11, 5, 11, 1, 1, 1, 1, 1, 1, 1, 11, 169, 169, 169, 169, 201, 201, 11, 11, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 499 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087368 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087368 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087368/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087368/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087368 Building REAL300004087369 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087369' /scratch/stefan/7774412/working/building/REAL300004087369 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087369 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087369/0 /scratch/stefan/7774412/working/building/REAL300004087369 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/458 `/scratch/stefan/7774412/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=C(C)C(C)=C2)S1) `REAL300004087369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087369 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=C(C)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 8, 1, 2, 2, 2, 2, 2, 2, 1] 17 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087369 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=C(C)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 8, 8, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087369 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087369 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087369/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087369 Building REAL300004087370 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087370' /scratch/stefan/7774412/working/building/REAL300004087370 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087370 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087370/0 /scratch/stefan/7774412/working/building/REAL300004087370 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/459 `/scratch/stefan/7774412/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CC[NH+](C)CC2)S1) `REAL300004087370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087370 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CC[NH+](C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 35, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087370 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CC[NH+](C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087370 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087370/1 /scratch/stefan/7774412/working/building/REAL300004087370 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/460 `/scratch/stefan/7774412/working/3D/460' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CC[NH+](C)CC2)S1) `REAL300004087370.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087370/1/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: REAL300004087370 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CC[NH+](C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 23, 19, 12, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 12, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087370 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CC[NH+](C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 9, 6, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 9, 27, 27, 29, 33, 33, 33, 33, 33, 33, 33, 33, 1, 2, 2, 2, 2, 2, 29, 29, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087370 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087370 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087370/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087370/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087370 Building REAL300004087371 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087371' /scratch/stefan/7774412/working/building/REAL300004087371 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087371 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087371/0 /scratch/stefan/7774412/working/building/REAL300004087371 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/461 `/scratch/stefan/7774412/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3CCCCC3=N2)S1) `REAL300004087371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087371 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3CCCCC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 10, 17, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087371 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3CCCCC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 9, 9, 9, 9, 10, 10] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087371 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087371 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087371/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087371 Building REAL300004087372 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087372' /scratch/stefan/7774412/working/building/REAL300004087372 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087372 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087372/0 /scratch/stefan/7774412/working/building/REAL300004087372 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/462 `/scratch/stefan/7774412/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C12) `REAL300004087372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087372 none CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 10, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 3, 2, 2, 2, 2, 2, 23, 23, 23] 39 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087372 none CC1=NN(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 6, 22, 22, 23, 23, 23, 23, 39, 39, 39, 23, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 23, 39, 39, 23, 23, 23, 1, 1, 1] 39 rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 18, 19, 20, 21, 22, 23, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087372 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087372/1 /scratch/stefan/7774412/working/building/REAL300004087372 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/463 `/scratch/stefan/7774412/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C12) `REAL300004087372.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087372/1/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: REAL300004087372 none CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 94, 40, 13, 40, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156, 94, 94, 2, 2, 2, 2, 2, 156, 156, 156] 201 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300004087372 none CC1=NN(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 26, 26, 64, 155, 155, 155, 201, 201, 201, 155, 155, 155, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 7, 201, 201, 155, 155, 155, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 21, 22, 23, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087372 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087372 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087372/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087372/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087372 Building REAL300004087373 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087373' /scratch/stefan/7774412/working/building/REAL300004087373 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087373 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087373/0 /scratch/stefan/7774412/working/building/REAL300004087373 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/464 `/scratch/stefan/7774412/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=C(F)C=C1C) `REAL300004087373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087373 none CCCOC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 37, 13, 7, 1, 7, 29, 29, 31, 40, 40, 40, 73, 99, 99, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 37, 37, 7, 31, 73, 73, 40, 40, 40, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [4, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 615 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087373 none CCCOC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 89, 40, 19, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 21, 40, 40, 23, 23, 40, 40, 40, 121, 121, 121, 121, 121, 89, 89, 21, 2, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40, 40] 201 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 602 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087373 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087373/1 /scratch/stefan/7774412/working/building/REAL300004087373 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/465 `/scratch/stefan/7774412/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=C(F)C=C1C) `REAL300004087373.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087373/1/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: REAL300004087373 none CCCOC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 35, 12, 6, 1, 6, 14, 14, 35, 72, 72, 72, 102, 131, 131, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 35, 35, 6, 102, 102, 72, 72, 72, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [4, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44]) total number of confs: 628 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087373 none CCCOC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=C(F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 128, 63, 45, 28, 11, 28, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 45, 72, 72, 47, 47, 72, 72, 72, 156, 156, 156, 156, 156, 128, 128, 45, 3, 3, 2, 2, 2, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 789 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087373 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087373 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087373/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087373/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087373 Building REAL300004087374 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087374' /scratch/stefan/7774412/working/building/REAL300004087374 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087374 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087374/0 /scratch/stefan/7774412/working/building/REAL300004087374 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/466 `/scratch/stefan/7774412/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NN2C)S1) `REAL300004087374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087374 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 29, 42, 42, 16, 12, 11, 1, 11, 1, 1, 1, 1, 13, 13, 1, 1, 1, 16, 16, 16, 16, 29, 29, 12, 1, 13, 13, 13, 13, 13, 2, 2, 2] 84 rigid atoms, others: [10, 12, 13, 14, 15, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 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: REAL300004087374 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 16, 16, 16, 55, 55, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 55, 55, 55, 55, 55, 16, 16, 16] 84 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 156 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087374 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 84, 84, 84, 55, 45, 44, 13, 44, 13, 13, 1, 1, 1, 1, 13, 13, 13, 55, 55, 55, 55, 84, 84, 45, 13, 1, 1, 1, 1, 1, 13, 13, 13] 84 rigid atoms, others: [32, 33, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36]) total number of confs: 288 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087374 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087374 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087374/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087374 Building REAL300004087375 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087375' /scratch/stefan/7774412/working/building/REAL300004087375 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087375 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087375/0 /scratch/stefan/7774412/working/building/REAL300004087375 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/467 `/scratch/stefan/7774412/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C[NH+]3CCCCC3)O2)S1) `REAL300004087375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087375 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C[NH+]3CCCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [16, 17, 17, 17, 29, 44, 44, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 1, 17, 17, 17, 17, 29, 29, 11, 1, 1, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 133 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087375 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C[NH+]3CCCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 17, 17, 17, 17, 55, 86, 86, 86, 86, 86, 86, 17, 1, 2, 2, 2, 2, 2, 2, 17, 17, 55, 55, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86] 133 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087375 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C[NH+]3CCCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 9, 6, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 133, 133, 133, 86, 55, 55, 17, 55, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 17, 86, 86, 86, 86, 133, 133, 55, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 133 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 476 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087375 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087375/1 /scratch/stefan/7774412/working/building/REAL300004087375 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/468 `/scratch/stefan/7774412/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3CCCCC3)O2)S1) `REAL300004087375.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087375 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3CCCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [9, 10, 10, 10, 17, 32, 32, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 8, 28, 28, 28, 28, 28, 1, 9, 10, 10, 10, 17, 17, 7, 1, 1, 8, 8, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 117 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 171 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087375 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3CCCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 40, 70, 70, 70, 70, 70, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 40, 40, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70] 117 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087375 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3CCCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 117, 117, 117, 70, 46, 46, 28, 46, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 28, 70, 70, 70, 70, 117, 117, 46, 28, 28, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 443 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087375 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087375 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087375/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087375/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087375 Building REAL300004087376 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087376' /scratch/stefan/7774412/working/building/REAL300004087376 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087376 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087376/0 /scratch/stefan/7774412/working/building/REAL300004087376 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/469 `/scratch/stefan/7774412/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(N(C)C)C=C2)S1) `REAL300004087376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087376 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 20, 25, 25, 11, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 9, 9, 6, 6, 11, 11, 11, 11, 20, 20, 11, 1, 1, 6, 6, 10, 10, 9, 10, 10, 9, 6, 6] 29 rigid atoms, others: [33, 34, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 138 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: REAL300004087376 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 17, 17, 11, 11, 19, 19, 17, 17, 1, 2, 2, 2, 2, 2, 2, 11, 11, 17, 17, 19, 19, 18, 19, 19, 18, 17, 17] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087376 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(N(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 8, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 25, 27, 27, 17, 17, 15, 6, 15, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 6, 6, 1, 1, 17, 17, 17, 17, 25, 25, 17, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 1, 1] 29 rigid atoms, others: [35, 36, 43, 44, 15, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087376 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087376 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087376/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087376 Building REAL300004087377 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087377' /scratch/stefan/7774412/working/building/REAL300004087377 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087377 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087377/0 /scratch/stefan/7774412/working/building/REAL300004087377 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/470 `/scratch/stefan/7774412/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2COC3=C(F)C=C(F)C=C3C2)S1) `REAL300004087377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087377 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2COC3=C(F)C=C(F)C=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 26, 26, 26, 18, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 26, 26, 13, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087377 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2COC3=C(F)C=C(F)C=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087377 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087377/1 /scratch/stefan/7774412/working/building/REAL300004087377 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/471 `/scratch/stefan/7774412/working/3D/471' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2COC3=C(F)C=C(F)C=C3C2)S1) `REAL300004087377.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087377/1/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: REAL300004087377 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2COC3=C(F)C=C(F)C=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 53, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087377 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2COC3=C(F)C=C(F)C=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 15, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 58, 58, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 1, 2, 2, 2, 2, 2, 148, 148, 148, 148, 148, 148, 148] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087377 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087377 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087377/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087377/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087377 Building REAL300004087378 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087378' /scratch/stefan/7774412/working/building/REAL300004087378 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087378 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087378/0 /scratch/stefan/7774412/working/building/REAL300004087378 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/472 `/scratch/stefan/7774412/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CC3)S2)S1) `REAL300004087378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087378 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CC3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [23, 24, 24, 24, 44, 71, 71, 24, 16, 13, 1, 13, 1, 1, 1, 1, 1, 8, 19, 19, 1, 24, 24, 24, 24, 44, 44, 16, 1, 1, 8, 8, 19, 19, 19, 19, 19] 134 rigid atoms, others: [10, 12, 13, 14, 15, 16, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 336 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087378 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CC3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 24, 24, 61, 79, 79, 24, 1, 2, 2, 2, 2, 2, 2, 24, 24, 61, 61, 79, 79, 79, 79, 79] 134 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087378 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CC3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 134, 134, 134, 79, 63, 61, 19, 61, 19, 19, 19, 5, 1, 1, 1, 1, 19, 79, 79, 79, 79, 134, 134, 63, 19, 19, 5, 5, 1, 1, 1, 1, 1] 134 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 512 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087378 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087378 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087378/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087378 Building REAL300004087379 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087379' /scratch/stefan/7774412/working/building/REAL300004087379 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087379 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087379/0 /scratch/stefan/7774412/working/building/REAL300004087379 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/473 `/scratch/stefan/7774412/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(OC)=CC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087379 none COC1=CC(OC)=CC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [54, 31, 31, 25, 31, 31, 53, 31, 9, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 31, 54, 54, 54, 31, 53, 53, 53, 31, 9, 9, 2, 3, 3, 2, 2, 2, 31] 150 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087379 none COC1=CC(OC)=CC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 12, 5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 1, 1, 1, 7, 17, 17, 17, 31, 31, 31, 58, 114, 114, 31, 31, 31, 1, 3, 3, 3, 1, 3, 3, 3, 1, 7, 7, 17, 58, 58, 31, 31, 31, 1] 150 rigid atoms, others: [1, 2, 3, 4, 5, 7, 8, 9, 40, 23, 27, 31] set([0, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 449 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087379 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087379 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087379/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087379 Building REAL300004087380 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087380' /scratch/stefan/7774412/working/building/REAL300004087380 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087380 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087380/0 /scratch/stefan/7774412/working/building/REAL300004087380 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/474 `/scratch/stefan/7774412/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3=CC=CC=C3)=N2)S1) `REAL300004087380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087380 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 28, 28, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 1, 7, 7, 1, 12, 13, 13, 13, 23, 23, 10, 1, 1, 1, 7, 7, 1, 7, 7] 44 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 123 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087380 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 12, 13, 13, 36, 36, 13, 36, 36, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 12, 36, 36, 13, 36, 36] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087380 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 44, 44, 44, 36, 32, 32, 7, 32, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 36, 36, 36, 36, 44, 44, 32, 7, 7, 7, 1, 1, 1, 1, 1] 44 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 124 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087380 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087380 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087380/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087380 Building REAL300004087381 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087381' /scratch/stefan/7774412/working/building/REAL300004087381 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087381 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087381/0 /scratch/stefan/7774412/working/building/REAL300004087381 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/475 `/scratch/stefan/7774412/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C([N+](=O)[O-])C(C)=C3N2)S1) `REAL300004087381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087381 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C([N+](=O)[O-])C(C)=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 27, 27, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 14, 15, 15, 15, 26, 26, 10, 1, 1, 1, 2, 2, 2, 1] 27 rigid atoms, others: [32, 33, 34, 38, 10, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087381 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C([N+](=O)[O-])C(C)=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 11, 11, 1, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 15, 15, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 15, 15, 15, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087381 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087381 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087381/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087381 Building REAL300004087382 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087382' /scratch/stefan/7774412/working/building/REAL300004087382 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087382 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087382/0 /scratch/stefan/7774412/working/building/REAL300004087382 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/476 `/scratch/stefan/7774412/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=CNN=C32)S1) `REAL300004087382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087382 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 30, 30, 30, 19, 14, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 30, 30, 14, 1, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 111 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087382 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 19] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087382 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087382/1 /scratch/stefan/7774412/working/building/REAL300004087382 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/477 `/scratch/stefan/7774412/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC3=CNN=C32)S1) `REAL300004087382.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087382/1/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: REAL300004087382 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 135, 135, 135, 116, 40, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 135, 135, 1, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087382 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 60, 60, 116, 116, 116, 116, 116, 116, 116, 1, 2, 2, 2, 2, 2, 116, 116, 116, 116, 116, 116, 116] 135 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087382 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087382 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087382/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087382/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087382 Building REAL300004087383 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087383' /scratch/stefan/7774412/working/building/REAL300004087383 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087383 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087383/0 /scratch/stefan/7774412/working/building/REAL300004087383 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/478 `/scratch/stefan/7774412/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCCCCCC2CC2)S1) `REAL300004087383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087383 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCCCCCC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 201, 201, 201, 107, 107, 107, 93, 107, 78, 49, 36, 21, 13, 7, 3, 1, 1, 1, 1, 107, 107, 107, 107, 201, 201, 107, 107, 107, 102, 102, 64, 64, 45, 45, 27, 27, 13, 13, 7, 7, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [46, 47, 48, 49, 50, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 1322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087383 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCCCCCC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 4, 6, 10, 15, 23, 33, 54, 107, 107, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 6, 6, 10, 10, 18, 18, 26, 26, 40, 40, 59, 59, 107, 107, 107, 107, 107] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087383 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087383 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087383/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087383 Building REAL300004087384 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087384' /scratch/stefan/7774412/working/building/REAL300004087384 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087384 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087384/0 /scratch/stefan/7774412/working/building/REAL300004087384 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/479 `/scratch/stefan/7774412/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCCOCC2)S1) `REAL300004087384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087384 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 11, 11, 7, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087384 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087384 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087384 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087384/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087384 Building REAL300004087385 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087385' /scratch/stefan/7774412/working/building/REAL300004087385 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087385 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087385/0 /scratch/stefan/7774412/working/building/REAL300004087385 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/480 `/scratch/stefan/7774412/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CCO[C@@H]2CCCCC3)S1) `REAL300004087385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087385 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CCO[C@@H]2CCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 19 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087385 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CCO[C@@H]2CCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 31 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087385 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087385/1 /scratch/stefan/7774412/working/building/REAL300004087385 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/481 `/scratch/stefan/7774412/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CCO[C@@H]2CCCCC3)S1) `REAL300004087385.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087385/1/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: REAL300004087385 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CCO[C@@H]2CCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 57, 57, 57, 41, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28]) total number of confs: 146 number of broken/clashed sets: 57 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087385 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CCO[C@@H]2CCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 7, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 120 number of broken/clashed sets: 57 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087385 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087385 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087385/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087385/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087385 Building REAL300004087386 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087386' /scratch/stefan/7774412/working/building/REAL300004087386 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087386 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087386/0 /scratch/stefan/7774412/working/building/REAL300004087386 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/482 `/scratch/stefan/7774412/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(C)(CC2)OC3)S1) `REAL300004087386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087386 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(C)(CC2)OC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 34, 33, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087386 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(C)(CC2)OC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087386 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087386/1 /scratch/stefan/7774412/working/building/REAL300004087386 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/483 `/scratch/stefan/7774412/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(C)(CC2)OC3)S1) `REAL300004087386.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087386/1/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: REAL300004087386 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(C)(CC2)OC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 201, 201, 201, 136, 41, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 201, 201, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 33, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087386 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(C)(CC2)OC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 43, 43, 136, 136, 136, 136, 136, 136, 136, 136, 1, 2, 2, 2, 2, 2, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087386 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087386 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087386/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087386/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087386 Building REAL300004087387 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087387' /scratch/stefan/7774412/working/building/REAL300004087387 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087387 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087387/0 /scratch/stefan/7774412/working/building/REAL300004087387 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/484 `/scratch/stefan/7774412/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCC(C)CC2)S1) `REAL300004087387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087387 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCC(C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 4, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087387 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCC(C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 2, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087387 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087387/1 /scratch/stefan/7774412/working/building/REAL300004087387 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/485 `/scratch/stefan/7774412/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCC(C)CC2)S1) `REAL300004087387.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087387/1/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: REAL300004087387 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCC(C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 184, 184, 184, 136, 28, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 184, 184, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1] 184 rigid atoms, others: [32, 33, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 35, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 463 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087387 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCC(C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 68, 68, 136, 136, 136, 136, 136, 136, 136, 1, 2, 2, 2, 2, 2, 136, 136, 136, 136, 136, 136, 131, 136, 136, 136, 136, 131, 136, 136, 136] 184 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087387 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087387 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087387/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087387/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087387 Building REAL300004087388 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087388' /scratch/stefan/7774412/working/building/REAL300004087388 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087388 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087388/0 /scratch/stefan/7774412/working/building/REAL300004087388 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/486 `/scratch/stefan/7774412/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)N=NS2)S1) `REAL300004087388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087388 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)N=NS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 29, 29, 16, 11, 9, 1, 9, 1, 1, 1, 2, 2, 1, 1, 1, 16, 16, 16, 16, 29, 29, 11, 2, 3, 3, 3, 3, 3, 3] 29 rigid atoms, others: [10, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300004087388 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)N=NS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087388 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087388 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087388/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087388 Building REAL300004087389 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087389' /scratch/stefan/7774412/working/building/REAL300004087389 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087389 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087389/0 /scratch/stefan/7774412/working/building/REAL300004087389 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/487 `/scratch/stefan/7774412/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=CNN=C32)S1) `REAL300004087389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087389 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 29, 29, 29, 15, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 119 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: REAL300004087389 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087389 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087389/1 /scratch/stefan/7774412/working/building/REAL300004087389 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/488 `/scratch/stefan/7774412/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=CNN=C32)S1) `REAL300004087389.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087389/1/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: REAL300004087389 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 119, 119, 119, 93, 37, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 119, 119, 1, 1, 1, 1, 1, 1, 1, 1, 1] 119 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087389 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=CNN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 48, 48, 93, 93, 93, 93, 93, 93, 93, 93, 1, 2, 2, 2, 2, 2, 93, 93, 93, 93, 93, 93, 93, 93, 93] 119 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087389 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087389 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087389/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087389/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087389 Building REAL300004087390 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087390' /scratch/stefan/7774412/working/building/REAL300004087390 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087390 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087390/0 /scratch/stefan/7774412/working/building/REAL300004087390 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/489 `/scratch/stefan/7774412/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2C=CSC2=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087390 none COC1=C2C=CSC2=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 9, 9, 13, 13, 13, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9] 19 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087390 none COC1=C2C=CSC2=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 14, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 13, 19, 19, 9, 9, 9, 1, 1, 3, 3, 3, 1, 1, 9, 13, 13, 9, 9, 9, 1, 1] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 35, 22, 23, 36, 27, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087390 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087390 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087390/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087390 Building REAL300004087391 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087391' /scratch/stefan/7774412/working/building/REAL300004087391 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087391 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087391/0 /scratch/stefan/7774412/working/building/REAL300004087391 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/490 `/scratch/stefan/7774412/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3(C)CC3)=C2)S1) `REAL300004087391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087391 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3(C)CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 13, 13, 13, 13, 23, 23, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1] 65 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 101 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087391 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3(C)CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 5, 13, 13, 37, 37, 37, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 11, 37, 37, 37, 37, 37, 37, 37, 13] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087391 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3(C)CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 65, 65, 65, 37, 29, 25, 5, 25, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 37, 37, 37, 37, 65, 65, 29, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 5] 65 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 260 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087391 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087391 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087391/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087391 Building REAL300004087392 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087392' /scratch/stefan/7774412/working/building/REAL300004087392 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087392 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087392/0 /scratch/stefan/7774412/working/building/REAL300004087392 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/491 `/scratch/stefan/7774412/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)C3)C=C2)S1) `REAL300004087392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087392 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 16, 16, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 35 rigid atoms, others: [32, 44, 10, 43, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087392 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 4, 7, 18, 18, 18, 18, 18, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 70 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087392 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 35, 35, 35, 18, 14, 12, 4, 12, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 18, 18, 18, 35, 35, 14, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5] 35 rigid atoms, others: [33, 34, 35, 36, 37, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44]) total number of confs: 157 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087392 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087392 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087392/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087392 Building REAL300004087393 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087393' /scratch/stefan/7774412/working/building/REAL300004087393 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087393 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087393/0 /scratch/stefan/7774412/working/building/REAL300004087393 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/492 `/scratch/stefan/7774412/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1) `REAL300004087393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087393 none C=CCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [60, 41, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 60, 60, 60, 41, 41, 13, 2, 2, 2, 2, 2, 2, 13] 88 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087393 none C=CCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 21, 48, 48, 13, 13, 13, 1, 1, 23, 23, 23, 7, 7, 1, 9, 21, 21, 13, 13, 13, 1] 88 rigid atoms, others: [33, 2, 3, 4, 5, 6, 19, 20, 26] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087393 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087393 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087393/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087393 Building REAL300004087394 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087394' /scratch/stefan/7774412/working/building/REAL300004087394 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087394 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087394/0 /scratch/stefan/7774412/working/building/REAL300004087394 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/493 `/scratch/stefan/7774412/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087394 none CC1=NOC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 9, 9, 9, 9, 4, 4, 2, 2, 2, 3, 3, 2, 2, 2, 9] 15 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087394 none CC1=NOC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 9, 9, 9, 1, 2, 2, 2, 5, 5, 9, 9, 9, 15, 15, 9, 9, 9, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087394 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087394 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087394/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087394 Building REAL300004087395 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087395' /scratch/stefan/7774412/working/building/REAL300004087395 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087395 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087395/0 /scratch/stefan/7774412/working/building/REAL300004087395 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/494 `/scratch/stefan/7774412/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)CCS3(=O)=O)S1) `REAL300004087395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087395 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)CCS3(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 11, 11, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087395 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)CCS3(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087395 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087395 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087395/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087395 Building REAL300004087396 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087396' /scratch/stefan/7774412/working/building/REAL300004087396 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087396 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087396/0 /scratch/stefan/7774412/working/building/REAL300004087396 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/495 `/scratch/stefan/7774412/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3CCC3)=C2)S1) `REAL300004087396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087396 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3CCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 29, 34, 34, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 11, 11, 11, 1, 16, 16, 16, 16, 29, 29, 11, 11, 11, 11, 11, 11, 11, 11, 1] 72 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087396 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3CCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 46, 46, 46, 16, 1, 2, 2, 2, 2, 2, 2, 46, 46, 46, 46, 46, 46, 46, 16] 72 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087396 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3CCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 72, 72, 72, 46, 35, 35, 11, 35, 11, 11, 11, 1, 1, 1, 1, 1, 11, 46, 46, 46, 46, 72, 72, 34, 1, 1, 1, 1, 1, 1, 1, 11] 72 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 255 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087396 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087396 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087396/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087396 Building REAL300004087397 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087397' /scratch/stefan/7774412/working/building/REAL300004087397 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087397 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087397/0 /scratch/stefan/7774412/working/building/REAL300004087397 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/496 `/scratch/stefan/7774412/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC=C2C2=CC=CC=C2)S1) `REAL300004087397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087397 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 32, 47, 47, 17, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 17, 18, 18, 18, 32, 32, 14, 1, 6, 6, 1, 6, 6] 51 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087397 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 17, 30, 30, 22, 30, 30, 1, 2, 2, 2, 2, 2, 2, 17, 30, 30, 25, 30, 30] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087397 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 51, 51, 51, 30, 26, 24, 6, 24, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 51, 51, 26, 6, 1, 1, 1, 1, 1] 51 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 21, 22, 31] 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]) total number of confs: 193 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087397 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087397 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087397/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087397 Building REAL300004087398 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087398' /scratch/stefan/7774412/working/building/REAL300004087398 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087398 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087398/0 /scratch/stefan/7774412/working/building/REAL300004087398 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/497 `/scratch/stefan/7774412/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC(F)=CC(F)=C2)S1) `REAL300004087398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087398 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 80, 80, 80, 48, 38, 35, 8, 35, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 80, 80, 38, 8, 8, 8, 8, 1, 1, 1] 80 rigid atoms, others: [33, 34, 35, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087398 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 23, 23, 49, 49, 49, 23, 49, 49, 49, 1, 2, 2, 2, 2, 2, 3, 23, 23, 23, 23, 49, 23, 49] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087398 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087398/1 /scratch/stefan/7774412/working/building/REAL300004087398 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/498 `/scratch/stefan/7774412/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC(F)=CC(F)=C2)S1) `REAL300004087398.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087398/1/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: REAL300004087398 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [157, 157, 157, 157, 201, 201, 201, 157, 70, 23, 8, 23, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 201, 201, 8, 8, 8, 8, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 525 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087398 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 12, 51, 51, 114, 114, 149, 149, 149, 114, 149, 149, 149, 1, 2, 2, 2, 2, 2, 114, 114, 114, 114, 149, 114, 149] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087398 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087398 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087398/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087398/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087398 Building REAL300004087399 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087399' /scratch/stefan/7774412/working/building/REAL300004087399 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087399 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087399/0 /scratch/stefan/7774412/working/building/REAL300004087399 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/499 `/scratch/stefan/7774412/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087399 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 105, 105, 105, 78, 78, 78, 73, 78, 22, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 78, 78, 78, 78, 105, 105, 78, 73, 73, 4, 4, 1, 1, 1, 1] 105 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 439 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087399 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 15, 45, 78, 78, 47, 58, 78, 78, 78, 78, 78, 1, 2, 2, 2, 2, 2, 2, 6, 6, 45, 45, 78, 78, 78, 78] 105 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087399 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087399/1 /scratch/stefan/7774412/working/building/REAL300004087399 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/500 `/scratch/stefan/7774412/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087399.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087399/1/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: REAL300004087399 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 201, 201, 201, 186, 140, 102, 53, 102, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 186, 186, 186, 186, 201, 201, 53, 53, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087399 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 29, 29, 53, 86, 149, 186, 186, 153, 178, 186, 186, 186, 186, 186, 1, 2, 2, 2, 2, 2, 53, 53, 149, 149, 186, 186, 186, 186] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087399 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087399 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087399/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087399/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087399 Building REAL300004087400 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087400' /scratch/stefan/7774412/working/building/REAL300004087400 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087400 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087400/0 /scratch/stefan/7774412/working/building/REAL300004087400 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/501 `/scratch/stefan/7774412/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2C(C)(C)C2(C)C)S1) `REAL300004087400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087400 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2C(C)(C)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 11, 11, 7, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 7, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 11 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 71 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087400 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2C(C)(C)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 2, 2, 5, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 3, 3, 2, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087400 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087400 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087400/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087400 Building REAL300004087401 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087401' /scratch/stefan/7774412/working/building/REAL300004087401 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087401 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087401/0 /scratch/stefan/7774412/working/building/REAL300004087401 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/502 `/scratch/stefan/7774412/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C=C3S2)S1) `REAL300004087401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087401 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 14, 27, 27, 27, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 27, 27, 11, 1, 1, 1, 1] 27 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087401 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 14, 14, 14, 13, 14, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087401 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087401 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087401/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087401 Building REAL300004087402 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087402' /scratch/stefan/7774412/working/building/REAL300004087402 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087402 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087402/0 /scratch/stefan/7774412/working/building/REAL300004087402 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/503 `/scratch/stefan/7774412/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1) `REAL300004087402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087402 none COC1=CC=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 14, 17, 17, 17, 28, 53, 53, 17, 17, 17, 1, 7, 13, 13, 13, 6, 7, 7, 1, 1, 14, 28, 28, 18, 18, 18, 7] 99 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087402 none COC1=CC=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 43, 43, 45, 57, 57, 57, 79, 99, 99, 57, 57, 57, 7, 1, 3, 3, 3, 1, 1, 1, 7, 7, 45, 79, 79, 57, 57, 57, 1] 99 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 25, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087402 none COC1=CC=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [73, 57, 57, 56, 57, 57, 17, 17, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 57, 73, 73, 73, 56, 57, 57, 17, 17, 2, 2, 2, 2, 2, 2, 57] 99 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 142 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087402 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087402 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087402/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087402 Building REAL300004087403 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087403' /scratch/stefan/7774412/working/building/REAL300004087403 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087403 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087403/0 /scratch/stefan/7774412/working/building/REAL300004087403 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/504 `/scratch/stefan/7774412/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC(F)=CC(F)=C1) `REAL300004087403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087403 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 1, 10, 25, 25, 25, 36, 36, 36, 60, 60, 60, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 10, 25, 60, 60, 36, 36, 36, 1, 1, 1] 60 rigid atoms, others: [2, 35, 36, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087403 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [38, 23, 3, 2, 3, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 25, 62, 62, 62, 25, 62, 62, 62, 38, 38, 38, 25, 2, 3, 3, 2, 2, 2, 62, 25, 62] 112 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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: 258 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087403 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087403/1 /scratch/stefan/7774412/working/building/REAL300004087403 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/505 `/scratch/stefan/7774412/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC(F)=CC(F)=C1) `REAL300004087403.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087403/1/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: REAL300004087403 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 10, 1, 10, 25, 25, 67, 157, 157, 157, 201, 201, 201, 157, 157, 157, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 10, 201, 201, 157, 157, 157, 1, 1, 1] 201 rigid atoms, others: [33, 2, 35, 34, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087403 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC(F)=CC(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 15, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 88, 43, 12, 43, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 88, 150, 150, 150, 88, 150, 150, 150, 113, 113, 113, 88, 2, 2, 2, 2, 2, 150, 88, 150] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087403 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087403 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087403/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087403/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087403 Building REAL300004087404 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087404' /scratch/stefan/7774412/working/building/REAL300004087404 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087404 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087404/0 /scratch/stefan/7774412/working/building/REAL300004087404 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/506 `/scratch/stefan/7774412/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NC2=CC(Cl)=C1) `REAL300004087404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087404 none COC1=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NC2=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [29, 22, 22, 22, 22, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 22, 22, 22, 22, 22, 22, 29, 29, 29, 22, 2, 2, 2, 2, 2, 2, 22, 22, 22] 37 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087404 none COC1=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NC2=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 1, 16, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 16, 22, 22, 22, 32, 37, 37, 22, 22, 22, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 16, 32, 32, 23, 23, 23, 1, 1, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 36, 28, 37, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087404 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087404 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087404/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087404 Building REAL300004087405 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087405' /scratch/stefan/7774412/working/building/REAL300004087405 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087405 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087405/0 /scratch/stefan/7774412/working/building/REAL300004087405 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/507 `/scratch/stefan/7774412/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CC(C)(C)C3)S1) `REAL300004087405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087405 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CC(C)(C)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 21, 21, 21, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 21 rigid atoms, others: [32, 33, 34, 42, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087405 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CC(C)(C)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087405 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087405 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087405/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087405 Building REAL300004087406 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087406' /scratch/stefan/7774412/working/building/REAL300004087406 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087406 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087406/0 /scratch/stefan/7774412/working/building/REAL300004087406 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/508 `/scratch/stefan/7774412/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC=C3)C=N2)S1) `REAL300004087406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087406 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC=C3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 21, 21, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 8, 8, 8, 8, 14, 14, 7, 1, 1, 3, 3, 3, 3, 3, 1] 21 rigid atoms, others: [32, 38, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 84 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087406 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC=C3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 8, 8, 7, 7, 13, 13, 13, 13, 13, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 13, 13, 13, 8] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087406 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC=C3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 21, 21, 21, 13, 11, 11, 3, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 13, 13, 13, 21, 21, 11, 3, 3, 1, 1, 1, 1, 1, 3] 21 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 76 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087406 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087406 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087406/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087406 Building REAL300004087407 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087407' /scratch/stefan/7774412/working/building/REAL300004087407 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087407 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087407/0 /scratch/stefan/7774412/working/building/REAL300004087407 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/509 `/scratch/stefan/7774412/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCO3)N=N2)S1) `REAL300004087407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087407 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCO3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 9, 15, 30, 30, 9, 5, 5, 1, 5, 1, 1, 1, 1, 8, 32, 32, 32, 32, 1, 1, 8, 9, 9, 9, 15, 15, 5, 1, 8, 8, 32, 32, 32, 32, 32, 32, 32] 116 rigid atoms, others: [10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 203 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087407 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCO3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 38, 69, 69, 69, 69, 8, 8, 1, 2, 2, 2, 2, 2, 2, 9, 38, 38, 69, 69, 69, 69, 69, 69, 69] 116 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087407 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCO3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 12, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 116, 116, 116, 69, 48, 48, 32, 48, 32, 32, 9, 1, 1, 1, 1, 1, 1, 32, 32, 69, 69, 69, 69, 116, 116, 48, 32, 9, 9, 1, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087407 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087407 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087407/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087407 Building REAL300004087408 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087408' /scratch/stefan/7774412/working/building/REAL300004087408 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087408 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087408/0 /scratch/stefan/7774412/working/building/REAL300004087408 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/510 `/scratch/stefan/7774412/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[C@@H](C)CC(C)(C)C2)S1) `REAL300004087408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087408 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[C@@H](C)CC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 35, 36, 36, 19, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 20, 20, 20, 35, 35, 13, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 36 rigid atoms, others: [35, 36, 44, 10, 43, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087408 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[C@@H](C)CC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 19, 19, 20, 20, 20, 19, 19, 20, 20, 20, 20, 20, 20, 19, 19] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087408 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087408 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087408/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087408 Building REAL300004087409 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087409' /scratch/stefan/7774412/working/building/REAL300004087409 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087409 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087409/0 /scratch/stefan/7774412/working/building/REAL300004087409 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/511 `/scratch/stefan/7774412/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(OC)=N1) `REAL300004087409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087409 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 9, 9, 9, 9, 11, 11, 11, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9] 19 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087409 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(OC)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'O.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 12, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 17, 19, 19, 9, 9, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8, 17, 17, 9, 9, 9, 2, 2, 2] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087409 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087409 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087409/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087409 Building REAL300004087410 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087410' /scratch/stefan/7774412/working/building/REAL300004087410 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087410 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087410/0 /scratch/stefan/7774412/working/building/REAL300004087410 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/512 `/scratch/stefan/7774412/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC(C)C)C(C)C)S1) `REAL300004087410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087410 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC(C)C)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 17, 17, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 17, 17, 17, 17] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 92 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087410 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087410 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087410/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087410 Building REAL300004087411 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087411' /scratch/stefan/7774412/working/building/REAL300004087411 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087411 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087411/0 /scratch/stefan/7774412/working/building/REAL300004087411 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/513 `/scratch/stefan/7774412/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CCC(C3)C2(C)C)S1) `REAL300004087411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087411 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CCC(C3)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 7 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42]) total number of confs: 39 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087411 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CCC(C3)C2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 33 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087411 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087411 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087411/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087411 Building REAL300004087412 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087412' /scratch/stefan/7774412/working/building/REAL300004087412 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087412 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087412/0 /scratch/stefan/7774412/working/building/REAL300004087412 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/514 `/scratch/stefan/7774412/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC(C(F)(F)F)=NC3=N2)S1) `REAL300004087412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087412 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC(C(F)(F)F)=NC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 7, 7, 13, 13, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 6, 7, 7, 7, 13, 13, 5, 1, 1] 13 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087412 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC(C(F)(F)F)=NC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'N.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 5, 15, 15, 15, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 7, 7, 7, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 7, 6] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087412 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087412 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087412/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087412 Building REAL300004087413 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087413' /scratch/stefan/7774412/working/building/REAL300004087413 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087413 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087413/0 /scratch/stefan/7774412/working/building/REAL300004087413 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/515 `/scratch/stefan/7774412/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1CCN(C2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)C1) `REAL300004087413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087413 none COCC1CCN(C2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 34, 34, 13, 13, 13, 1, 1, 4, 13, 13, 13, 12, 12, 4, 4, 4, 4, 4, 1, 1, 9, 25, 25, 13, 13, 13, 1, 1, 4, 4] 128 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 45, 46, 24, 25, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 178 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087413 none COCC1CCN(C2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 17, 17, 20, 28, 28, 28, 55, 63, 63, 28, 28, 28, 4, 4, 1, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 4, 4, 20, 55, 55, 28, 28, 28, 4, 4, 1, 1] 128 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 47, 48, 35, 36, 26] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 288 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087413 none COCC1CCN(C2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 128 conformations in input total number of sets (complete confs): 128 using faster count positions algorithm for large data unique positions, atoms: [68, 67, 28, 28, 28, 28, 11, 11, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 28, 68, 68, 68, 67, 67, 28, 28, 28, 28, 28, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 28, 28] 128 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 276 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087413 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087413 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087413/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087413 Building REAL300004087414 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087414' /scratch/stefan/7774412/working/building/REAL300004087414 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087414 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087414/0 /scratch/stefan/7774412/working/building/REAL300004087414 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/516 `/scratch/stefan/7774412/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087414 none COC1=CC=CC(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 10, 10, 6, 10, 10, 10, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 17, 17, 10, 10, 10, 11, 11, 11, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087414 none COC1=CC=CC(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 10, 10, 10, 20, 25, 25, 10, 10, 10, 3, 3, 3, 1, 1, 1, 2, 2, 2, 8, 20, 20, 11, 11, 11] 27 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087414 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087414 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087414/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087414 Building REAL300004087415 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087415' /scratch/stefan/7774412/working/building/REAL300004087415 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087415 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087415/0 /scratch/stefan/7774412/working/building/REAL300004087415 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/517 `/scratch/stefan/7774412/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC=C2C(C)C)S1) `REAL300004087415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087415 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC=C2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 11, 11, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 11, 11, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2] 11 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087415 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC=C2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087415 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087415 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087415/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087415 Building REAL300004087416 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087416' /scratch/stefan/7774412/working/building/REAL300004087416 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087416 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087416/0 /scratch/stefan/7774412/working/building/REAL300004087416 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/518 `/scratch/stefan/7774412/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC2)S1) `REAL300004087416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087416 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 45, 65, 65, 23, 14, 13, 1, 13, 1, 1, 13, 13, 13, 13, 1, 1, 23, 23, 23, 23, 45, 45, 14, 13, 13, 13, 1, 1, 1, 1] 111 rigid atoms, others: [32, 33, 10, 12, 13, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 270 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087416 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 23, 91, 91, 91, 91, 23, 23, 1, 2, 2, 2, 2, 2, 3, 91, 91, 91, 23, 23, 23, 23] 111 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 169 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087416 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 111, 111, 111, 91, 72, 71, 13, 71, 1, 1, 1, 1, 1, 1, 13, 13, 91, 91, 91, 91, 111, 111, 72, 1, 1, 1, 13, 13, 13, 13] 111 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 329 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087416 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087416/1 /scratch/stefan/7774412/working/building/REAL300004087416 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/519 `/scratch/stefan/7774412/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC2)S1) `REAL300004087416.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087416 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [132, 132, 132, 132, 181, 182, 182, 132, 47, 12, 1, 12, 1, 1, 11, 11, 11, 11, 1, 1, 132, 132, 132, 132, 181, 181, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [32, 10, 12, 13, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 494 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087416 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 13, 50, 50, 132, 157, 157, 157, 157, 132, 132, 1, 2, 2, 2, 2, 2, 157, 157, 157, 132, 132, 132, 132] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087416 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [157, 157, 157, 157, 201, 201, 201, 157, 85, 42, 11, 42, 1, 1, 1, 1, 1, 1, 11, 11, 157, 157, 157, 157, 201, 201, 1, 1, 1, 11, 11, 11, 11] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 533 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087416 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087416 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087416/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087416/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087416 Building REAL300004087417 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087417' /scratch/stefan/7774412/working/building/REAL300004087417 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087417 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087417/0 /scratch/stefan/7774412/working/building/REAL300004087417 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/520 `/scratch/stefan/7774412/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(COCC1=CC=CC=C1)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087417 none CCC(C)(COCC1=CC=CC=C1)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 2, 8, 8, 23, 43, 116, 139, 139, 128, 139, 139, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 12, 12, 12, 12, 9, 9, 9, 23, 23, 116, 116, 139, 139, 139, 139, 139, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 590 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087417 none CCC(C)(COCC1=CC=CC=C1)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 104, 42, 104, 17, 3, 1, 1, 1, 1, 1, 1, 1, 104, 123, 123, 123, 139, 139, 139, 199, 201, 201, 139, 139, 139, 130, 130, 130, 130, 130, 105, 105, 105, 42, 42, 3, 3, 1, 1, 1, 1, 1, 123, 199, 199, 140, 140, 140] 201 rigid atoms, others: [11, 6, 38, 7, 8, 9, 10, 39, 12, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47, 48]) total number of confs: 1061 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087417 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087417/1 /scratch/stefan/7774412/working/building/REAL300004087417 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/521 `/scratch/stefan/7774412/working/3D/521' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(COCC1=CC=CC=C1)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087417.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087417/1/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: REAL300004087417 none CCC(C)(COCC1=CC=CC=C1)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 60, 30, 60, 60, 79, 102, 174, 188, 188, 175, 188, 188, 13, 30, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 79, 79, 174, 174, 188, 188, 188, 188, 188, 2, 2, 2, 2, 2] 201 rigid atoms, others: [15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 950 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087417 none CCC(C)(COCC1=CC=CC=C1)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 35, 22, 35, 13, 3, 1, 1, 1, 1, 1, 1, 1, 35, 68, 68, 126, 188, 188, 188, 201, 201, 201, 188, 188, 188, 51, 51, 51, 50, 50, 35, 35, 35, 22, 22, 3, 3, 1, 1, 1, 1, 1, 201, 201, 188, 188, 188] 201 rigid atoms, others: [11, 6, 38, 7, 8, 9, 10, 39, 12, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087417 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087417 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087417/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087417/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087417 Building REAL300004087418 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087418' /scratch/stefan/7774412/working/building/REAL300004087418 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087418 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087418/0 /scratch/stefan/7774412/working/building/REAL300004087418 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/522 `/scratch/stefan/7774412/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1) `REAL300004087418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087418 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 155, 158, 158, 82, 64, 59, 15, 59, 5, 3, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 21, 23, 23, 82, 82, 82, 82, 155, 155, 64, 15, 6, 6, 3, 3, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 158 rigid atoms, others: [39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48]) total number of confs: 714 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087418 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 54, 69, 82, 82, 77, 82, 82, 22, 35, 35, 28, 35, 35, 1, 2, 2, 2, 2, 2, 2, 22, 54, 54, 69, 69, 82, 82, 82, 82, 82, 35, 35, 35, 35, 35] 158 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 435 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087418 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 66, 74, 74, 35, 22, 20, 4, 20, 1, 4, 10, 15, 23, 23, 19, 23, 23, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 66, 66, 22, 4, 10, 10, 15, 15, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1] 158 rigid atoms, others: [12, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 385 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087418 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087418/1 /scratch/stefan/7774412/working/building/REAL300004087418 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/523 `/scratch/stefan/7774412/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1) `REAL300004087418.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087418/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087418 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 179, 184, 184, 137, 60, 18, 8, 18, 3, 3, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 11, 13, 13, 137, 137, 137, 137, 179, 179, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 184 rigid atoms, others: [38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 46, 47]) total number of confs: 510 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087418 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 60, 60, 99, 133, 133, 137, 137, 135, 137, 137, 99, 114, 114, 113, 114, 114, 1, 2, 2, 2, 2, 2, 99, 133, 133, 133, 133, 137, 137, 137, 137, 137, 114, 114, 114, 114, 114] 184 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087418 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CCC2=CC=CC=C2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 150, 162, 162, 114, 41, 11, 4, 11, 1, 4, 9, 9, 13, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 150, 150, 4, 9, 9, 9, 9, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1] 184 rigid atoms, others: [44, 43, 12, 45, 46, 47, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 465 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087418 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087418 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087418/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087418/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087418 Building REAL300004087419 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087419' /scratch/stefan/7774412/working/building/REAL300004087419 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087419 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087419/0 /scratch/stefan/7774412/working/building/REAL300004087419 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/524 `/scratch/stefan/7774412/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CC2)S1) `REAL300004087419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087419 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 18, 19, 19, 10, 8, 7, 1, 7, 1, 1, 9, 9, 9, 9, 9, 1, 1, 10, 10, 10, 10, 18, 18, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1] 44 rigid atoms, others: [37, 38, 39, 40, 10, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087419 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 10, 24, 24, 24, 24, 24, 10, 10, 1, 2, 2, 2, 2, 2, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087419 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 44, 44, 44, 24, 22, 22, 9, 22, 1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 44, 44, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 44 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087419 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087419/1 /scratch/stefan/7774412/working/building/REAL300004087419 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/525 `/scratch/stefan/7774412/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CC2)S1) `REAL300004087419.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087419 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 141, 141, 141, 99, 34, 7, 1, 7, 1, 1, 8, 8, 8, 8, 8, 1, 1, 99, 99, 99, 99, 141, 141, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 142 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 401 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087419 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 58, 58, 99, 105, 105, 105, 105, 105, 99, 99, 1, 2, 2, 2, 2, 2, 105, 105, 105, 105, 105, 105, 105, 105, 105, 99, 99, 99, 99] 142 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087419 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 142, 142, 142, 105, 41, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 8, 8, 105, 105, 105, 105, 142, 142, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 142 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087419 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087419 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087419/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087419/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087419 Building REAL300004087420 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087420' /scratch/stefan/7774412/working/building/REAL300004087420 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087420 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087420/0 /scratch/stefan/7774412/working/building/REAL300004087420 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/526 `/scratch/stefan/7774412/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[N@@H+](C(C)(C)C)C[C@@H]2C(F)(F)F)S1) `REAL300004087420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087420 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[N@@H+](C(C)(C)C)C[C@@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1] 2 rigid atoms, others: [35, 36, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 47, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 11 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: REAL300004087420 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[N@@H+](C(C)(C)C)C[C@@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 32, 28] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 15 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087420 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087420/1 /scratch/stefan/7774412/working/building/REAL300004087420 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/527 `/scratch/stefan/7774412/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[N@H+](C(C)(C)C)C[C@@H]2C(F)(F)F)S1) `REAL300004087420.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087420/1/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: REAL300004087420 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[N@H+](C(C)(C)C)C[C@@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1] 3 rigid atoms, others: [35, 36, 10, 46, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 47, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 13 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087420 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[N@H+](C(C)(C)C)C[C@@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 33, 7, 8, 9, 32, 28] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 21 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087420 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087420 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087420/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087420/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087420 Building REAL300004087421 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087421' /scratch/stefan/7774412/working/building/REAL300004087421 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087421 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087421/0 /scratch/stefan/7774412/working/building/REAL300004087421 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/528 `/scratch/stefan/7774412/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3CCC(C2)S3)S1) `REAL300004087421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087421 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3CCC(C2)S3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 25 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087421 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3CCC(C2)S3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087421 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087421/1 /scratch/stefan/7774412/working/building/REAL300004087421 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/529 `/scratch/stefan/7774412/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3CCC(C2)S3)S1) `REAL300004087421.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087421/1/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: REAL300004087421 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3CCC(C2)S3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 201, 201, 201, 135, 37, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087421 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3CCC(C2)S3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 49, 49, 135, 135, 135, 135, 135, 135, 135, 135, 1, 2, 2, 2, 2, 2, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087421 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087421 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087421/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087421/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087421 Building REAL300004087422 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087422' /scratch/stefan/7774412/working/building/REAL300004087422 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087422 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087422/0 /scratch/stefan/7774412/working/building/REAL300004087422 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/530 `/scratch/stefan/7774412/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3CCC(C2)S3(=O)=O)S1) `REAL300004087422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087422 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3CCC(C2)S3(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 25 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087422 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3CCC(C2)S3(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087422 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087422/1 /scratch/stefan/7774412/working/building/REAL300004087422 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/531 `/scratch/stefan/7774412/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3CCC(C2)S3(=O)=O)S1) `REAL300004087422.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087422/1/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: REAL300004087422 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3CCC(C2)S3(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 65, 65, 65, 49, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 65, 65, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087422 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3CCC(C2)S3(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 2, 2, 2, 2, 2, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087422 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087422 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087422/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087422/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087422 Building REAL300004087423 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087423' /scratch/stefan/7774412/working/building/REAL300004087423 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087423 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087423/0 /scratch/stefan/7774412/working/building/REAL300004087423 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/532 `/scratch/stefan/7774412/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C(F)(F)F)S1) `REAL300004087423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087423 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 25, 25, 25, 14, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 25, 11, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 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: REAL300004087423 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 63 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087423 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087423/1 /scratch/stefan/7774412/working/building/REAL300004087423 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/533 `/scratch/stefan/7774412/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C(F)(F)F)S1) `REAL300004087423.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087423/1/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: REAL300004087423 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28]) total number of confs: 449 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087423 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 69, 69, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 1, 2, 2, 2, 3, 3, 163, 163, 163, 163] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087423 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087423 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087423/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087423/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087423 Building REAL300004087424 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087424' /scratch/stefan/7774412/working/building/REAL300004087424 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087424 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087424/0 /scratch/stefan/7774412/working/building/REAL300004087424 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/534 `/scratch/stefan/7774412/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CS2)=NO1) `REAL300004087424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087424 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CS2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 14, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 25, 25, 79, 79, 79, 79, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 79, 79, 79] 137 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087424 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CS2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 14, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 14, 25, 25, 25, 47, 63, 63, 25, 24, 24, 1, 1, 12, 12, 12, 12, 1, 1, 2, 2, 2, 14, 47, 47, 25, 25, 25, 12, 12, 12] 137 rigid atoms, others: [0, 1, 2, 3, 16, 17, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 277 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087424 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CS2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 14, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 49, 49, 55, 79, 79, 79, 137, 137, 137, 79, 79, 79, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 55, 137, 137, 79, 79, 79, 1, 1, 1] 137 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 525 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087424 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087424 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087424/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087424 Building REAL300004087425 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087425' /scratch/stefan/7774412/working/building/REAL300004087425 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087425 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087425/0 /scratch/stefan/7774412/working/building/REAL300004087425 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/535 `/scratch/stefan/7774412/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)CC2=CC(Cl)=CC(Cl)=C2)S1) `REAL300004087425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087425 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)CC2=CC(Cl)=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 76, 76, 76, 48, 41, 38, 11, 38, 5, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 76, 76, 41, 11, 33, 5, 5, 1, 1, 1] 228 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 342 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087425 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)CC2=CC(Cl)=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 228 conformations in input total number of sets (complete confs): 228 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 18, 41, 44, 44, 44, 44, 44, 44, 44, 1, 2, 2, 2, 2, 2, 2, 18, 54, 41, 41, 44, 44, 44] 228 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 259 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087425 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087425/1 /scratch/stefan/7774412/working/building/REAL300004087425 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/536 `/scratch/stefan/7774412/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)CC2=CC(Cl)=CC(Cl)=C2)S1) `REAL300004087425.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087425/1/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: REAL300004087425 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)CC2=CC(Cl)=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 201, 201, 201, 159, 72, 32, 10, 32, 5, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 201, 201, 10, 30, 5, 5, 1, 1, 1] 603 rigid atoms, others: [33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 559 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087425 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)CC2=CC(Cl)=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 40, 40, 107, 107, 148, 154, 154, 154, 154, 154, 154, 154, 1, 2, 2, 2, 2, 2, 107, 321, 148, 148, 154, 154, 154] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 957 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087425 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087425 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087425/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087425/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087425 Building REAL300004087426 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087426' /scratch/stefan/7774412/working/building/REAL300004087426 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087426 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087426/0 /scratch/stefan/7774412/working/building/REAL300004087426 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/537 `/scratch/stefan/7774412/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC3=C2OCC3)S1) `REAL300004087426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087426 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC3=C2OCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 153, 153, 153, 93, 69, 66, 12, 66, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 153, 153, 69, 12, 36, 1, 1, 1, 1, 1, 1, 1] 459 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087426 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC3=C2OCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 459 conformations in input total number of sets (complete confs): 459 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 25, 25, 93, 93, 93, 93, 93, 93, 93, 93, 1, 2, 2, 2, 2, 2, 2, 25, 75, 93, 93, 93, 93, 93, 93, 93] 459 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087426 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087426/1 /scratch/stefan/7774412/working/building/REAL300004087426 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/538 `/scratch/stefan/7774412/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC3=C2OCC3)S1) `REAL300004087426.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087426/1/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: REAL300004087426 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC3=C2OCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 201, 201, 201, 159, 72, 33, 7, 33, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 201, 201, 7, 21, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 540 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087426 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC3=C2OCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 43, 43, 107, 107, 159, 159, 159, 159, 159, 159, 159, 159, 1, 2, 2, 2, 3, 3, 107, 321, 159, 159, 159, 159, 159, 159, 159] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 829 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087426 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087426 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087426/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087426/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087426 Building REAL300004087427 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087427' /scratch/stefan/7774412/working/building/REAL300004087427 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087427 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087427/0 /scratch/stefan/7774412/working/building/REAL300004087427 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/539 `/scratch/stefan/7774412/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC(O)C2CCCC2)S1) `REAL300004087427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087427 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(O)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 12, 12, 12, 8, 8, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 8, 7, 7, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 68 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087427 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(O)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 6, 6, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 4, 4, 6, 18, 8, 8, 8, 8, 8, 8, 8, 8, 8] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087427 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087427 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087427/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087427 Building REAL300004087428 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087428' /scratch/stefan/7774412/working/building/REAL300004087428 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087428 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087428/0 /scratch/stefan/7774412/working/building/REAL300004087428 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/540 `/scratch/stefan/7774412/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(CC(F)(F)F)C=C2)S1) `REAL300004087428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087428 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(CC(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 22, 40, 40, 13, 12, 12, 1, 12, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 13, 13, 13, 13, 22, 22, 12, 9, 9, 1, 1] 81 rigid atoms, others: [32, 10, 12, 13, 14, 15, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300004087428 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(CC(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 47, 47, 47, 47, 13, 13, 1, 2, 2, 2, 2, 2, 2, 47, 47, 13, 13] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087428 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087428 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087428/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087428 Building REAL300004087429 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087429' /scratch/stefan/7774412/working/building/REAL300004087429 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087429 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087429/0 /scratch/stefan/7774412/working/building/REAL300004087429 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/541 `/scratch/stefan/7774412/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(OC(F)F)C=C2)S1) `REAL300004087429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087429 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(OC(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 10, 16, 16, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 28, 46, 46, 7, 7, 7, 7, 7, 7, 10, 10, 7, 1, 1, 7, 7, 47, 7, 7] 80 rigid atoms, others: [34, 35, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087429 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(OC(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 12, 12, 7, 8, 40, 57, 57, 12, 12, 1, 2, 2, 2, 2, 2, 2, 7, 7, 12, 12, 58, 12, 12] 80 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087429 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(OC(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 12, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 19, 37, 37, 12, 12, 11, 7, 11, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 10, 28, 28, 1, 1, 12, 12, 12, 12, 19, 19, 12, 7, 7, 1, 1, 28, 1, 1] 80 rigid atoms, others: [36, 37, 39, 40, 15, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 217 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087429 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087429 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087429/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087429 Building REAL300004087430 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087430' /scratch/stefan/7774412/working/building/REAL300004087430 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087430 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087430/0 /scratch/stefan/7774412/working/building/REAL300004087430 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/542 `/scratch/stefan/7774412/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2(C)CCCC2)S1) `REAL300004087430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087430 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2(C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087430 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2(C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087430 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087430/1 /scratch/stefan/7774412/working/building/REAL300004087430 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/543 `/scratch/stefan/7774412/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2(C)CCCC2)S1) `REAL300004087430.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087430/1/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: REAL300004087430 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2(C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 195, 195, 195, 163, 108, 69, 21, 69, 10, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 195, 195, 21, 21, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 195 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 545 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087430 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2(C)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 10, 29, 29, 56, 102, 163, 163, 163, 163, 163, 1, 2, 2, 2, 3, 3, 56, 56, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163] 195 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 503 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087430 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087430 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087430/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087430/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087430 Building REAL300004087431 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087431' /scratch/stefan/7774412/working/building/REAL300004087431 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087431 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087431/0 /scratch/stefan/7774412/working/building/REAL300004087431 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/544 `/scratch/stefan/7774412/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CC=C3C=N2)S1) `REAL300004087431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087431 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CC=C3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 9, 9, 9, 16, 16, 16, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 8, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087431 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CC=C3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 8, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087431 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087431 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087431/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087431 Building REAL300004087432 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087432' /scratch/stefan/7774412/working/building/REAL300004087432 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087432 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087432/0 /scratch/stefan/7774412/working/building/REAL300004087432 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/545 `/scratch/stefan/7774412/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2CC(F)(F)C2)S1) `REAL300004087432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087432 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2CC(F)(F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 19, 19, 19, 12, 12, 12, 10, 12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 12, 10, 10, 6, 6, 1, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087432 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2CC(F)(F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 10, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 12, 12, 12, 12, 12] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087432 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087432 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087432/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087432 Building REAL300004087433 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087433' /scratch/stefan/7774412/working/building/REAL300004087433 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087433 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087433/0 /scratch/stefan/7774412/working/building/REAL300004087433 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/546 `/scratch/stefan/7774412/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2COC3=CC(Cl)=CC=C3C2)S1) `REAL300004087433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087433 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2COC3=CC(Cl)=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 16, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 26, 27, 27, 13, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 26, 26, 12, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087433 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2COC3=CC(Cl)=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 16, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087433 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087433/1 /scratch/stefan/7774412/working/building/REAL300004087433 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/547 `/scratch/stefan/7774412/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2COC3=CC(Cl)=CC=C3C2)S1) `REAL300004087433.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087433/1/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: REAL300004087433 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2COC3=CC(Cl)=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 16, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 201, 201, 201, 161, 65, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087433 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2COC3=CC(Cl)=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 1, 1, 1, 16, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 64, 64, 161, 161, 161, 161, 161, 161, 161, 161, 161, 161, 1, 2, 2, 2, 2, 2, 161, 161, 161, 161, 161, 161, 161, 161] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087433 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087433 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087433/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087433/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087433 Building REAL300004087434 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087434' /scratch/stefan/7774412/working/building/REAL300004087434 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087434 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087434/0 /scratch/stefan/7774412/working/building/REAL300004087434 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/548 `/scratch/stefan/7774412/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCC(C)(C)O2)S1) `REAL300004087434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087434 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCC(C)(C)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 27, 27, 27, 16, 16, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 27, 27, 16, 7, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 27 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087434 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCC(C)(C)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087434 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087434 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087434/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087434 Building REAL300004087435 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087435' /scratch/stefan/7774412/working/building/REAL300004087435 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087435 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087435/0 /scratch/stefan/7774412/working/building/REAL300004087435 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/549 `/scratch/stefan/7774412/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCOC(C)(C)C2)S1) `REAL300004087435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087435 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCOC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 22, 23, 23, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 22, 22, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 23 rigid atoms, others: [38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087435 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCOC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 11, 11] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087435 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087435 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087435/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087435 Building REAL300004087436 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087436' /scratch/stefan/7774412/working/building/REAL300004087436 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087436 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087436/0 /scratch/stefan/7774412/working/building/REAL300004087436 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/550 `/scratch/stefan/7774412/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCC(F)(F)F)S1) `REAL300004087436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087436 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 10, 14, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 14, 14, 18, 18] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087436 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087436 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087436/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087436 Building REAL300004087437 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087437' /scratch/stefan/7774412/working/building/REAL300004087437 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087437 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087437/0 /scratch/stefan/7774412/working/building/REAL300004087437 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/551 `/scratch/stefan/7774412/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[C@@H](OC(F)F)C2)S1) `REAL300004087437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087437 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[C@@H](OC(F)F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 15, 15, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 15, 15, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 17, 17, 1, 8, 8, 8, 8, 13, 13, 8, 1, 1, 17, 1, 1] 37 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087437 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2C[C@@H](OC(F)F)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'F', 'F', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 15, 15, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 19, 37, 37, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 37, 8, 8] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087437 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087437 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087437/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087437 Building REAL300004087438 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087438' /scratch/stefan/7774412/working/building/REAL300004087438 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087438 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087438/0 /scratch/stefan/7774412/working/building/REAL300004087438 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/552 `/scratch/stefan/7774412/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C(C)(C)C)=N2)S1) `REAL300004087438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087438 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 15, 21, 21, 21, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 14, 15, 15, 15, 20, 21, 11, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 31 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087438 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 15, 23, 23, 23, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087438 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087438 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087438/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087438 Building REAL300004087439 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087439' /scratch/stefan/7774412/working/building/REAL300004087439 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087439 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087439/0 /scratch/stefan/7774412/working/building/REAL300004087439 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/553 `/scratch/stefan/7774412/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N3C=NC=N3)=N2)S1) `REAL300004087439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087439 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N3C=NC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 18, 19, 19, 12, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 12, 13, 13, 13, 18, 18, 11, 1, 1, 1, 3, 3] 21 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087439 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N3C=NC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 15, 15, 15, 15, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 15, 15] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087439 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(N3C=NC=N3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 21, 21, 21, 15, 14, 12, 3, 12, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 15, 21, 21, 14, 2, 3, 3, 1, 1] 21 rigid atoms, others: [33, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 75 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087439 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087439 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087439/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087439 Building REAL300004087440 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087440' /scratch/stefan/7774412/working/building/REAL300004087440 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087440 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087440/0 /scratch/stefan/7774412/working/building/REAL300004087440 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/554 `/scratch/stefan/7774412/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1) `REAL300004087440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087440 none COC1=CC=CC=C1C1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [27, 12, 12, 12, 1, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 14, 20, 20, 20, 40, 76, 76, 20, 20, 20, 1, 27, 27, 27, 12, 12, 12, 12, 1, 14, 40, 41, 21, 21, 21] 175 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087440 none COC1=CC=CC=C1C1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 73, 73, 76, 96, 97, 97, 169, 175, 175, 97, 97, 96, 12, 3, 3, 3, 1, 1, 1, 1, 12, 76, 169, 169, 97, 97, 97] 175 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087440 none COC1=CC=CC=C1C1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [112, 96, 96, 96, 75, 96, 96, 20, 20, 20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 112, 112, 112, 97, 96, 96, 96, 20, 2, 2, 2, 2, 2, 2] 175 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 284 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087440 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087440 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087440/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087440 Building REAL300004087441 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087441' /scratch/stefan/7774412/working/building/REAL300004087441 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087441 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087441/0 /scratch/stefan/7774412/working/building/REAL300004087441 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/555 `/scratch/stefan/7774412/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3N(CCNS3(=O)=O)N=C2)S1) `REAL300004087441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087441 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3N(CCNS3(=O)=O)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 8, 14, 11, 11, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 8, 8, 11, 11, 11, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 11, 11, 6, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087441 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3N(CCNS3(=O)=O)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 8, 14, 11, 11, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 7, 7, 7, 8, 8, 8, 8, 8, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 8, 8, 8, 8, 7] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087441 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087441 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087441/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087441 Building REAL300004087442 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087442' /scratch/stefan/7774412/working/building/REAL300004087442 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087442 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087442/0 /scratch/stefan/7774412/working/building/REAL300004087442 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/556 `/scratch/stefan/7774412/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C(C)(C)C)S1) `REAL300004087442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087442 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 19, 19, 19, 12, 9, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 19, 19, 9, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 19 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087442 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NN2C(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 50 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087442 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087442 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087442/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087442 Building REAL300004087443 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087443' /scratch/stefan/7774412/working/building/REAL300004087443 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087443 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087443/0 /scratch/stefan/7774412/working/building/REAL300004087443 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/557 `/scratch/stefan/7774412/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C2CC2)S1) `REAL300004087443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087443 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 27, 27, 27, 14, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 27, 27, 10, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3] 27 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087443 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087443 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 27, 27, 27, 14, 10, 9, 3, 9, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 14, 14, 14, 14, 27, 27, 10, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 27 rigid atoms, others: [35, 36, 37, 38, 39, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 111 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087443 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087443 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087443/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087443 Building REAL300004087444 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087444' /scratch/stefan/7774412/working/building/REAL300004087444 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087444 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087444/0 /scratch/stefan/7774412/working/building/REAL300004087444 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/558 `/scratch/stefan/7774412/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(CCCC2CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1) `REAL300004087444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087444 none CC1=NC2=C(CCCC2CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 2, 2, 2, 2, 2, 2] 42 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087444 none CC1=NC2=C(CCCC2CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18, 18, 20, 23, 23, 23, 42, 42, 42, 23, 23, 23, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 42, 42, 23, 23, 23] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 33, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087444 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087444 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087444/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087444 Building REAL300004087445 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087445' /scratch/stefan/7774412/working/building/REAL300004087445 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087445 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087445/0 /scratch/stefan/7774412/working/building/REAL300004087445 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/559 `/scratch/stefan/7774412/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CN=CC=C12) `REAL300004087445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087445 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CN=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 9, 9, 9, 7, 7, 2, 2, 2, 2, 2, 2, 7, 7, 7] 11 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087445 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CN=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 9, 11, 11, 7, 7, 7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 7, 9, 9, 7, 7, 7, 1, 1, 1] 11 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 36, 38, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087445 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087445 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087445/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087445 Building REAL300004087446 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087446' /scratch/stefan/7774412/working/building/REAL300004087446 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087446 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087446/0 /scratch/stefan/7774412/working/building/REAL300004087446 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/560 `/scratch/stefan/7774412/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC1=CC=CC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087446 none CCCCCC1=CC=CC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 95, 63, 33, 17, 17, 15, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 14, 105, 105, 105, 105, 105, 95, 95, 63, 63, 33, 33, 17, 17, 17, 5, 5, 1, 3, 3, 2, 2, 2, 17] 201 rigid atoms, others: [41, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) total number of confs: 512 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087446 none CCCCCC1=CC=CC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 6, 2, 1, 1, 1, 1, 1, 1, 1, 6, 17, 17, 17, 17, 17, 17, 33, 49, 49, 17, 17, 17, 1, 13, 13, 13, 13, 13, 10, 10, 6, 6, 2, 2, 1, 1, 1, 6, 6, 17, 33, 33, 17, 17, 17, 1] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 47, 24, 4, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 268 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087446 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087446 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087446/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087446 Building REAL300004087447 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087447' /scratch/stefan/7774412/working/building/REAL300004087447 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087447 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087447/0 /scratch/stefan/7774412/working/building/REAL300004087447 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/561 `/scratch/stefan/7774412/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1) `REAL300004087447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087447 none CCCCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [61, 53, 43, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 61, 61, 61, 61, 60, 53, 53, 43, 43, 13, 2, 2, 2, 2, 2, 2] 100 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087447 none CCCCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [20, 14, 8, 1, 1, 1, 1, 1, 1, 10, 10, 10, 14, 13, 14, 25, 38, 38, 13, 13, 13, 1, 21, 21, 21, 20, 20, 14, 14, 8, 8, 1, 10, 25, 25, 14, 14, 14] 100 rigid atoms, others: [3, 4, 5, 6, 7, 8, 21, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087447 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087447 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087447/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087447 Building REAL300004087448 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087448' /scratch/stefan/7774412/working/building/REAL300004087448 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087448 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087448/0 /scratch/stefan/7774412/working/building/REAL300004087448 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/562 `/scratch/stefan/7774412/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(COC(C)(C)C)S2)S1) `REAL300004087448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087448 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(COC(C)(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 12, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 27, 35, 35, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 8, 18, 20, 21, 20, 1, 14, 14, 14, 14, 27, 27, 11, 1, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 21] 69 rigid atoms, others: [10, 12, 13, 14, 15, 16, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 201 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087448 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(COC(C)(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 12, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 40, 46, 46, 46, 46, 14, 1, 2, 2, 2, 2, 2, 2, 14, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087448 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087448 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087448/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087448 Building REAL300004087449 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087449' /scratch/stefan/7774412/working/building/REAL300004087449 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087449 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087449/0 /scratch/stefan/7774412/working/building/REAL300004087449 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/563 `/scratch/stefan/7774412/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1) `REAL300004087449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087449 none CCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 12, 26, 26, 26, 25, 25, 2, 2, 2, 2, 2, 2, 13] 43 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087449 none CCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 23, 28, 28, 12, 12, 12, 1, 1, 8, 8, 8, 8, 8, 9, 23, 23, 13, 13, 13, 1] 43 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087449 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087449 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087449/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087449 Building REAL300004087450 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087450' /scratch/stefan/7774412/working/building/REAL300004087450 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087450 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087450/0 /scratch/stefan/7774412/working/building/REAL300004087450 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/564 `/scratch/stefan/7774412/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C2CC2)S1) `REAL300004087450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087450 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 29, 40, 40, 15, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 7, 7, 15, 16, 16, 16, 29, 29, 12, 1, 1, 7, 7, 7, 7, 7] 56 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087450 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 32, 32, 1, 2, 2, 2, 2, 2, 2, 15, 15, 32, 32, 32, 32, 32] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087450 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 56, 56, 56, 32, 26, 23, 7, 23, 7, 7, 7, 7, 1, 1, 1, 1, 32, 32, 32, 32, 56, 56, 26, 7, 7, 1, 1, 1, 1, 1] 56 rigid atoms, others: [32, 33, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 218 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087450 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087450 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087450/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087450 Building REAL300004087451 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087451' /scratch/stefan/7774412/working/building/REAL300004087451 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087451 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087451/0 /scratch/stefan/7774412/working/building/REAL300004087451 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/565 `/scratch/stefan/7774412/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1) `REAL300004087451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087451 none COC1=CC(F)=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 7, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 12, 12, 12, 15, 15, 15, 28, 49, 49, 15, 15, 15, 1, 7, 11, 11, 11, 6, 7, 1, 1, 12, 28, 28, 16, 16, 16, 7] 100 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087451 none COC1=CC(F)=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 46, 46, 46, 60, 60, 60, 86, 100, 100, 60, 60, 60, 7, 1, 3, 3, 3, 1, 1, 7, 7, 46, 86, 86, 60, 60, 60, 1] 100 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 40, 26, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087451 none COC1=CC(F)=CC(N2C=CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [73, 60, 60, 59, 60, 60, 60, 15, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 60, 73, 73, 73, 59, 60, 15, 15, 2, 2, 2, 2, 2, 2, 60] 100 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087451 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087451 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087451/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087451 Building REAL300004087452 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087452' /scratch/stefan/7774412/working/building/REAL300004087452 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087452 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087452/0 /scratch/stefan/7774412/working/building/REAL300004087452 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/566 `/scratch/stefan/7774412/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3CC3CC2)S1) `REAL300004087452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087452 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3CC3CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 103 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087452 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3CC3CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 58 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087452 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087452 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087452/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087452 Building REAL300004087453 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087453' /scratch/stefan/7774412/working/building/REAL300004087453 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087453 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087453/0 /scratch/stefan/7774412/working/building/REAL300004087453 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/567 `/scratch/stefan/7774412/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCC=CCC2)S1) `REAL300004087453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087453 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCC=CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 26, 26, 26, 15, 15, 13, 6, 13, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 26, 26, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087453 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCC=CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 2, 2, 11, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 2, 11, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087453 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087453 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087453/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087453 Building REAL300004087454 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087454' /scratch/stefan/7774412/working/building/REAL300004087454 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087454 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087454/0 /scratch/stefan/7774412/working/building/REAL300004087454 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/568 `/scratch/stefan/7774412/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CSC[C@@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087454 none CC(=O)N1CSC[C@@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [29, 17, 29, 17, 17, 17, 17, 3, 17, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 29, 29, 29, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2] 47 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087454 none CC(=O)N1CSC[C@@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 10, 17, 17, 17, 32, 38, 38, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 10, 32, 32, 17, 17, 17] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087454 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087454/1 /scratch/stefan/7774412/working/building/REAL300004087454 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/569 `/scratch/stefan/7774412/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CSC[C@@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087454.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087454/1/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: REAL300004087454 none CC(=O)N1CSC[C@@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [105, 92, 105, 92, 92, 92, 92, 58, 92, 12, 58, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 105, 105, 105, 92, 92, 92, 92, 2, 2, 1, 1, 1] 133 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087454 none CC(=O)N1CSC[C@@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 92, 92, 92, 131, 132, 132, 92, 92, 92, 4, 4, 4, 1, 1, 1, 1, 131, 131, 92, 92, 92] 133 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 374 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087454 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087454 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087454/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087454/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087454 Building REAL300004087455 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087455' /scratch/stefan/7774412/working/building/REAL300004087455 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087455 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087455/0 /scratch/stefan/7774412/working/building/REAL300004087455 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/570 `/scratch/stefan/7774412/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CCCC(C)(C)C2)S1) `REAL300004087455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087455 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CCCC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 23, 23, 23, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 23, 23, 9, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 23 rigid atoms, others: [38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37]) total number of confs: 95 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087455 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CCCC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 44 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087455 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087455 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087455/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087455 Building REAL300004087456 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087456' /scratch/stefan/7774412/working/building/REAL300004087456 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087456 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087456/0 /scratch/stefan/7774412/working/building/REAL300004087456 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/571 `/scratch/stefan/7774412/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCO1) `REAL300004087456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087456 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 9, 2, 2, 2, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 22, 18, 18, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 31 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087456 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 1, 1, 5, 5, 5, 9, 9, 9, 17, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 10, 9, 9, 4, 4, 5, 17, 17, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 31 rigid atoms, others: [33, 2, 3, 4, 37, 35, 39, 40, 34, 17, 18, 19, 20, 21, 36, 38] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087456 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087456/1 /scratch/stefan/7774412/working/building/REAL300004087456 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/572 `/scratch/stefan/7774412/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCCO1) `REAL300004087456.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087456/1/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: REAL300004087456 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [138, 125, 113, 60, 13, 60, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 113, 113, 113, 113, 113, 138, 138, 138, 125, 125, 2, 2, 2, 2, 2, 113, 113, 113, 113, 113, 113, 113, 113] 164 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087456 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 1, 1, 1, 5, 5, 26, 113, 113, 113, 159, 164, 164, 113, 113, 113, 1, 1, 1, 1, 1, 11, 11, 11, 5, 5, 159, 159, 113, 113, 113, 1, 1, 1, 1, 1, 1, 1, 1] 164 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 39, 34, 17, 18, 19, 20, 21, 36, 38] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087456 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087456 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087456/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087456/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087456 Building REAL300004087457 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087457' /scratch/stefan/7774412/working/building/REAL300004087457 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087457 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087457/0 /scratch/stefan/7774412/working/building/REAL300004087457 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/573 `/scratch/stefan/7774412/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(F)(F)F)C(C)=CC=C2)S1) `REAL300004087457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087457 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(F)(F)F)C(C)=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 2, 2, 2, 1, 1, 1] 5 rigid atoms, others: [33, 34, 35, 10, 12, 13, 14, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087457 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(F)(F)F)C(C)=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 15, 15, 15, 1, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087457 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087457 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087457/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087457 Building REAL300004087458 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087458' /scratch/stefan/7774412/working/building/REAL300004087458 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087458 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087458/0 /scratch/stefan/7774412/working/building/REAL300004087458 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/574 `/scratch/stefan/7774412/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N(C)C)C=CC=C3S2)S1) `REAL300004087458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087458 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N(C)C)C=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 36, 37, 37, 18, 12, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 18, 19, 19, 19, 36, 36, 12, 1, 3, 3, 3, 3, 3, 3, 1, 1, 1] 37 rigid atoms, others: [38, 39, 40, 10, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087458 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(N(C)C)C=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 19, 19, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 20, 20, 20, 20, 20, 20, 18, 18, 18] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087458 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087458 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087458/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087458 Building REAL300004087459 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087459' /scratch/stefan/7774412/working/building/REAL300004087459 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087459 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087459/0 /scratch/stefan/7774412/working/building/REAL300004087459 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/575 `/scratch/stefan/7774412/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=NC=C2)CC3)S1) `REAL300004087459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087459 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=NC=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 18, 18, 8, 6, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 8, 8, 8, 8, 15, 15, 6, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 39, 40, 41, 10, 12, 13, 14, 15, 16, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087459 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=NC=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 18, 18, 13, 18, 18, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 18, 18, 18, 18, 8, 8, 8, 8] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087459 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=NC=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 23, 23, 23, 18, 15, 13, 6, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 18, 18, 18, 23, 23, 15, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 23 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087459 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087459 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087459/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087459 Building REAL300004087460 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087460' /scratch/stefan/7774412/working/building/REAL300004087460 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087460 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087460/0 /scratch/stefan/7774412/working/building/REAL300004087460 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/576 `/scratch/stefan/7774412/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(F)C=C2F)S1) `REAL300004087460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087460 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(F)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 12, 15, 15, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 4, 6, 6, 6, 6, 7, 7, 7, 7, 12, 12, 7, 1, 1, 6, 6, 6] 19 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 73 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087460 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(F)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 7, 7, 13, 13, 13] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087460 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(F)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 15, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 19, 19, 19, 13, 13, 13, 6, 13, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 19, 19, 13, 6, 6, 1, 1, 1] 19 rigid atoms, others: [34, 35, 36, 15, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087460 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087460 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087460/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087460 Building REAL300004087461 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087461' /scratch/stefan/7774412/working/building/REAL300004087461 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087461 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087461/0 /scratch/stefan/7774412/working/building/REAL300004087461 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/577 `/scratch/stefan/7774412/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2CCCCCCC2)S1) `REAL300004087461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087461 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2CCCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 67, 67, 67, 39, 33, 28, 8, 28, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 67, 67, 33, 8, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 299 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087461 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2CCCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 19, 19, 37, 39, 39, 39, 39, 39, 37, 1, 2, 2, 2, 2, 2, 3, 19, 57, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 228 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087461 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087461/1 /scratch/stefan/7774412/working/building/REAL300004087461 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/578 `/scratch/stefan/7774412/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2CCCCCCC2)S1) `REAL300004087461.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087461/1/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: REAL300004087461 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2CCCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 201, 201, 201, 152, 62, 25, 7, 25, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 201, 201, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 563 number of broken/clashed sets: 603 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087461 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2CCCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 45, 45, 104, 104, 152, 152, 152, 152, 152, 152, 148, 1, 2, 2, 2, 2, 2, 104, 312, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 911 number of broken/clashed sets: 603 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087461 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087461 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087461/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087461/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087461 Building REAL300004087462 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087462' /scratch/stefan/7774412/working/building/REAL300004087462 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087462 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087462/0 /scratch/stefan/7774412/working/building/REAL300004087462 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/579 `/scratch/stefan/7774412/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3CCCCC3=NC(C)=C2)S1) `REAL300004087462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087462 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3CCCCC3=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 21, 21, 21, 12, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 38, 40, 23, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087462 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3CCCCC3=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087462 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087462 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087462/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087462 Building REAL300004087463 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087463' /scratch/stefan/7774412/working/building/REAL300004087463 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087463 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087463/0 /scratch/stefan/7774412/working/building/REAL300004087463 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/580 `/scratch/stefan/7774412/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2=CC=CC=C2C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087463 none COC1=CC=C(C2=CC=CC=C2C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 17, 17, 17, 17, 31, 37, 37, 17, 17, 17, 5, 9, 9, 9, 5, 5, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 17, 17, 17, 5] 37 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087463 none COC1=CC=C(C2=CC=CC=C2C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 5, 1, 1, 7, 7, 9, 9, 9, 9, 17, 23, 23, 9, 9, 9, 1, 3, 3, 3, 1, 1, 5, 5, 1, 5, 5, 5, 5, 9, 17, 17, 9, 9, 9, 1] 37 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 13, 14, 46, 27, 31] set([0, 7, 8, 9, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087463 none COC1=CC=C(C2=CC=CC=C2C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 17, 17, 9, 17, 17, 17, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 11, 11, 11, 4, 9, 17, 17, 14, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 9] 37 rigid atoms, others: [16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087463 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087463 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087463/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087463 Building REAL300004087464 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087464' /scratch/stefan/7774412/working/building/REAL300004087464 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087464 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087464/0 /scratch/stefan/7774412/working/building/REAL300004087464 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/581 `/scratch/stefan/7774412/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CN=C2)S1) `REAL300004087464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087464 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 15, 5, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 5, 5, 1, 1, 1, 1] 15 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 39 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087464 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 2, 7, 7, 15, 15, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087464 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087464 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087464/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087464 Building REAL300004087465 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087465' /scratch/stefan/7774412/working/building/REAL300004087465 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087465 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087465/0 /scratch/stefan/7774412/working/building/REAL300004087465 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/582 `/scratch/stefan/7774412/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(O)(C3=CC=CC=C3)C2)S1) `REAL300004087465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087465 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(O)(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 22, 22, 22, 13, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 13, 13, 13, 13, 22, 22, 9, 1, 1, 1, 1, 1, 6, 3, 3, 2, 3, 3, 1, 1] 90 rigid atoms, others: [32, 33, 34, 35, 10, 43, 12, 13, 14, 15, 16, 17, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41]) total number of confs: 95 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087465 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(O)(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 18, 18, 18, 18, 18, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 39, 18, 18, 18, 18, 18, 13, 13] 90 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 108 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087465 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC(O)(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 30, 30, 30, 18, 14, 13, 3, 13, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 30, 30, 14, 3, 3, 3, 3, 3, 9, 1, 1, 1, 1, 1, 3, 3] 90 rigid atoms, others: [37, 38, 39, 40, 41, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 124 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087465 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087465 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087465/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087465 Building REAL300004087466 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087466' /scratch/stefan/7774412/working/building/REAL300004087466 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087466 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087466/0 /scratch/stefan/7774412/working/building/REAL300004087466 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/583 `/scratch/stefan/7774412/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1) `REAL300004087466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087466 none CCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [27, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 14, 14, 14, 27, 53, 53, 14, 14, 14, 10, 10, 27, 27, 27, 27, 27, 10, 1, 1, 1, 1, 8, 27, 27, 14, 14, 14, 10] 142 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 281 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087466 none CCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 39, 39, 41, 61, 61, 61, 84, 98, 98, 61, 61, 61, 1, 1, 7, 7, 7, 7, 7, 1, 10, 10, 10, 10, 41, 84, 84, 61, 61, 61, 1] 142 rigid atoms, others: [32, 1, 2, 3, 4, 5, 43, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087466 none CCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [116, 61, 61, 61, 14, 14, 14, 14, 14, 14, 4, 14, 3, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 61, 61, 116, 116, 116, 116, 116, 61, 14, 14, 14, 14, 3, 2, 2, 1, 1, 1, 61] 142 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087466 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087466/1 /scratch/stefan/7774412/working/building/REAL300004087466 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/584 `/scratch/stefan/7774412/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1) `REAL300004087466.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087466/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087466 none CCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 24, 71, 71, 71, 98, 111, 111, 71, 71, 71, 5, 5, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 98, 98, 71, 71, 71, 5] 201 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 36] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 344 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087466 none CCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 40, 94, 94, 94, 119, 128, 128, 94, 94, 94, 1, 1, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 119, 119, 94, 94, 94, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 42, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087466 none CCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 94, 94, 94, 71, 71, 71, 71, 71, 71, 44, 71, 13, 44, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 94, 94, 154, 154, 154, 154, 154, 94, 71, 71, 71, 71, 2, 2, 2, 2, 2, 94] 201 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 621 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087466 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087466 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087466/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087466/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087466 Building REAL300004087467 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087467' /scratch/stefan/7774412/working/building/REAL300004087467 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087467 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087467/0 /scratch/stefan/7774412/working/building/REAL300004087467 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/585 `/scratch/stefan/7774412/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1) `REAL300004087467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087467 none COCCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 50, 39, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 17, 33, 33, 9, 9, 9, 10, 10, 77, 77, 77, 50, 50, 39, 39, 10, 1, 1, 1, 1, 9, 17, 17, 9, 9, 9, 10] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087467 none COCCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 12, 8, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 33, 33, 42, 42, 42, 42, 72, 99, 99, 42, 42, 42, 1, 1, 32, 32, 32, 12, 12, 8, 8, 1, 10, 10, 10, 10, 42, 72, 72, 42, 42, 42, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 47, 36, 27, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 470 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087467 none COCCN1C=C([C@@H]2OCC[C@H]2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 138, 118, 42, 42, 42, 9, 9, 9, 9, 9, 9, 2, 9, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 42, 42, 151, 151, 151, 138, 138, 118, 118, 42, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 42] 201 rigid atoms, others: [44, 45, 46, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47]) total number of confs: 568 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087467 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087467/1 /scratch/stefan/7774412/working/building/REAL300004087467 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/586 `/scratch/stefan/7774412/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1) `REAL300004087467.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087467/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087467 none COCCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 23, 23, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 61, 61, 61, 77, 102, 102, 61, 61, 61, 7, 7, 37, 37, 37, 23, 23, 23, 23, 7, 1, 1, 1, 1, 77, 77, 61, 61, 61, 7] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 38] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) total number of confs: 370 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087467 none COCCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 22, 22, 49, 123, 123, 123, 144, 159, 159, 123, 123, 123, 1, 1, 16, 16, 16, 7, 7, 7, 7, 1, 7, 7, 7, 7, 144, 144, 123, 123, 123, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 46, 36, 27, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087467 none COCCN1C=C([C@@H]2OCC[C@H]2C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 183, 183, 123, 123, 123, 61, 61, 61, 61, 61, 61, 23, 61, 12, 23, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 123, 123, 188, 188, 188, 183, 183, 183, 183, 123, 61, 61, 61, 61, 2, 2, 2, 2, 2, 123] 201 rigid atoms, others: [16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 618 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087467 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087467 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087467/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087467/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087467 Building REAL300004087468 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087468' /scratch/stefan/7774412/working/building/REAL300004087468 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087468 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087468/0 /scratch/stefan/7774412/working/building/REAL300004087468 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/587 `/scratch/stefan/7774412/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1) `REAL300004087468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087468 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 34, 49, 49, 18, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 18, 18, 18, 18, 34, 34, 13, 1, 1, 1, 1, 11, 11, 11, 11, 11] 75 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 204 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087468 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 18, 18, 18, 18, 18, 18, 18, 55, 55, 55, 55, 55, 1, 2, 2, 2, 2, 2, 3, 18, 18, 18, 18, 55, 55, 55, 55, 55] 75 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087468 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 75, 75, 75, 55, 44, 38, 11, 38, 11, 11, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 75, 75, 44, 11, 11, 11, 11, 1, 2, 2, 2, 1] 75 rigid atoms, others: [36, 40, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087468 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087468/1 /scratch/stefan/7774412/working/building/REAL300004087468 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/588 `/scratch/stefan/7774412/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1) `REAL300004087468.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087468 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 160, 172, 172, 114, 31, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 114, 114, 114, 114, 160, 160, 1, 1, 1, 1, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 485 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087468 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 57, 57, 114, 114, 114, 114, 114, 114, 114, 164, 164, 164, 164, 164, 1, 2, 2, 2, 2, 2, 114, 114, 114, 114, 164, 164, 164, 164, 164] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087468 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CN(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 201, 201, 201, 164, 92, 37, 9, 37, 9, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 201, 201, 9, 9, 9, 9, 1, 2, 2, 2, 1] 201 rigid atoms, others: [35, 39, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 506 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087468 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087468 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087468/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087468/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087468 Building REAL300004087469 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087469' /scratch/stefan/7774412/working/building/REAL300004087469 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087469 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087469/0 /scratch/stefan/7774412/working/building/REAL300004087469 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/589 `/scratch/stefan/7774412/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1) `REAL300004087469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087469 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 5, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 37, 55, 55, 20, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 20, 20, 20, 20, 37, 37, 13, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 93 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 226 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087469 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 5, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 20, 20, 20, 20, 20, 20, 20, 67, 67, 67, 67, 67, 67, 1, 2, 2, 2, 2, 2, 3, 20, 20, 20, 20, 67, 67, 67, 67, 67, 67, 67] 93 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087469 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 5, 8, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 93, 93, 93, 67, 55, 44, 9, 44, 9, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 93, 93, 55, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 1] 93 rigid atoms, others: [43, 17, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 341 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087469 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087469/1 /scratch/stefan/7774412/working/building/REAL300004087469 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/590 `/scratch/stefan/7774412/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1) `REAL300004087469.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087469 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 5, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 165, 170, 170, 125, 43, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 125, 125, 125, 125, 165, 165, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087469 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 5, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 63, 63, 125, 125, 125, 125, 125, 125, 125, 168, 168, 168, 168, 168, 168, 1, 2, 2, 2, 2, 2, 125, 125, 125, 125, 168, 168, 168, 168, 168, 168, 168] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 439 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087469 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=C(C)N(C)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 5, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 201, 201, 201, 168, 76, 33, 9, 33, 9, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [42, 17, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 484 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087469 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087469 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087469/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087469/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087469 Building REAL300004087470 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087470' /scratch/stefan/7774412/working/building/REAL300004087470 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087470 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087470/0 /scratch/stefan/7774412/working/building/REAL300004087470 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/591 `/scratch/stefan/7774412/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1) `REAL300004087470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087470 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [10, 11, 11, 11, 21, 32, 32, 11, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 10, 11, 11, 11, 21, 21, 8, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 9] 54 rigid atoms, others: [35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087470 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 35, 35, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 29, 29, 35, 35, 35, 35, 35, 35, 35] 54 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 28] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 115 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087470 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 52, 53, 53, 29, 24, 20, 6, 20, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 52, 52, 24, 6, 6, 6, 6, 6, 6, 1, 1, 5, 5, 5, 5, 5, 5, 5] 54 rigid atoms, others: [41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 232 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087470 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087470/1 /scratch/stefan/7774412/working/building/REAL300004087470 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/592 `/scratch/stefan/7774412/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1) `REAL300004087470.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087470 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 145, 165, 165, 106, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 106, 106, 106, 106, 145, 145, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 486 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: REAL300004087470 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 62, 62, 106, 106, 106, 106, 106, 106, 106, 106, 152, 152, 152, 152, 152, 163, 163, 1, 2, 2, 2, 2, 2, 106, 106, 106, 106, 106, 106, 152, 152, 163, 163, 163, 163, 163, 163, 163] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 28] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 448 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087470 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 201, 201, 201, 152, 62, 22, 6, 22, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 4, 4, 152, 152, 152, 152, 201, 201, 6, 6, 6, 6, 6, 6, 1, 1, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [40, 41, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 537 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087470 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087470 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087470/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087470/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087470 Building REAL300004087471 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087471' /scratch/stefan/7774412/working/building/REAL300004087471 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087471 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087471/0 /scratch/stefan/7774412/working/building/REAL300004087471 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/593 `/scratch/stefan/7774412/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(F)C=C3)=C2)S1) `REAL300004087471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087471 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(F)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 27, 33, 33, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 2, 2, 4, 4, 1, 14, 14, 14, 14, 27, 27, 11, 2, 2, 2, 4, 4, 4, 4, 1] 33 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087471 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(F)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 20, 20, 20, 20, 14] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087471 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(F)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 33, 33, 33, 20, 15, 15, 4, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 20, 20, 20, 20, 33, 33, 15, 4, 4, 4, 1, 1, 1, 1, 4] 33 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 121 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087471 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087471 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087471/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087471 Building REAL300004087472 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087472' /scratch/stefan/7774412/working/building/REAL300004087472 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087472 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087472/0 /scratch/stefan/7774412/working/building/REAL300004087472 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/594 `/scratch/stefan/7774412/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1) `REAL300004087472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087472 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [13, 14, 14, 14, 24, 30, 30, 14, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 13, 14, 14, 14, 24, 24, 10, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 44 rigid atoms, others: [33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087472 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 25, 25, 25, 25, 25] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087472 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 44, 44, 44, 25, 18, 15, 5, 15, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 44, 44, 18, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 2] 44 rigid atoms, others: [39, 40, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087472 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087472/1 /scratch/stefan/7774412/working/building/REAL300004087472 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/595 `/scratch/stefan/7774412/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1) `REAL300004087472.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087472/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087472 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 145, 159, 159, 110, 34, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 110, 110, 110, 110, 145, 145, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42]) total number of confs: 422 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087472 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 62, 62, 110, 110, 110, 110, 110, 110, 110, 110, 163, 163, 163, 163, 163, 1, 2, 2, 2, 2, 2, 110, 110, 110, 110, 110, 110, 163, 163, 163, 163, 163] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 428 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087472 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCCO[C@H]2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 63, 25, 6, 25, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 201, 201, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2] 201 rigid atoms, others: [38, 39, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 485 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087472 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087472 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087472/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087472/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087472 Building REAL300004087473 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087473' /scratch/stefan/7774412/working/building/REAL300004087473 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087473 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087473/0 /scratch/stefan/7774412/working/building/REAL300004087473 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/596 `/scratch/stefan/7774412/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)OC(C(C)C)=C2)S1) `REAL300004087473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087473 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)OC(C(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 23, 23, 45, 54, 54, 23, 13, 11, 1, 11, 1, 1, 1, 2, 2, 1, 1, 1, 4, 4, 1, 22, 23, 23, 23, 45, 45, 13, 2, 3, 3, 3, 3, 3, 3, 4, 5, 5, 5, 4, 4, 4, 1] 78 rigid atoms, others: [44, 10, 12, 13, 14, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 261 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087473 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)OC(C(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 23, 25, 25, 22, 22, 22, 43, 43, 22, 1, 2, 2, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25, 25, 43, 43, 43, 43, 43, 43, 43, 22] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087473 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087473 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087473/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087473 Building REAL300004087474 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087474' /scratch/stefan/7774412/working/building/REAL300004087474 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087474 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087474/0 /scratch/stefan/7774412/working/building/REAL300004087474 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/597 `/scratch/stefan/7774412/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(N2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)C=C1) `REAL300004087474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087474 none COC1=CC=C(N2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 2, 6, 6, 1, 1, 1, 1, 1, 12, 12, 14, 17, 17, 17, 30, 43, 43, 17, 17, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 1, 14, 30, 30, 18, 18, 18, 7, 7] 45 rigid atoms, others: [5, 6, 7, 8, 9, 22, 23, 31] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087474 none COC1=CC=C(N2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 22, 21, 24, 29, 29, 29, 45, 45, 45, 29, 29, 29, 6, 6, 1, 1, 1, 1, 1, 1, 1, 7, 23, 45, 45, 29, 29, 29, 1, 1] 45 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: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087474 none COC1=CC=C(N2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 27, 29, 29, 17, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 17, 29, 29, 29, 29, 29, 29, 29, 17, 2, 2, 2, 2, 2, 2, 29, 29] 45 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087474 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087474 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087474/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087474 Building REAL300004087475 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087475' /scratch/stefan/7774412/working/building/REAL300004087475 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087475 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087475/0 /scratch/stefan/7774412/working/building/REAL300004087475 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/598 `/scratch/stefan/7774412/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2=CC=CC=C2)S1) `REAL300004087475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087475 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 17, 17, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 7, 7, 7, 7, 11, 11, 7, 5, 5, 4, 4, 4, 4, 4] 17 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 81 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087475 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 7, 7, 13, 13, 11, 13, 13, 1, 2, 2, 2, 2, 2, 2, 4, 4, 13, 13, 13, 13, 13] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087475 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 17, 17, 17, 13, 13, 13, 11, 13, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 17, 17, 13, 11, 11, 1, 1, 1, 1, 1] 17 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087475 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087475/1 /scratch/stefan/7774412/working/building/REAL300004087475 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/599 `/scratch/stefan/7774412/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2=CC=CC=C2)S1) `REAL300004087475.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087475 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 170, 201, 201, 125, 55, 31, 8, 31, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 125, 125, 125, 125, 170, 170, 8, 8, 6, 6, 1, 6, 6] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 629 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087475 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 10, 32, 32, 68, 125, 125, 125, 125, 125, 157, 157, 125, 157, 157, 1, 2, 2, 2, 3, 3, 68, 68, 157, 157, 125, 157, 157] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 517 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087475 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 201, 201, 201, 157, 92, 53, 19, 53, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 201, 201, 19, 19, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 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]) total number of confs: 569 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087475 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087475 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087475/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087475/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087475 Building REAL300004087476 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087476' /scratch/stefan/7774412/working/building/REAL300004087476 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087476 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087476/0 /scratch/stefan/7774412/working/building/REAL300004087476 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/600 `/scratch/stefan/7774412/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CC3)O2)S1) `REAL300004087476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087476 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 16, 29, 32, 32, 16, 13, 12, 1, 12, 1, 1, 1, 1, 1, 12, 12, 1, 15, 16, 16, 16, 29, 29, 13, 1, 1, 12, 12, 12, 12, 12] 67 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087476 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 39, 39, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 39, 39, 39, 39, 39] 66 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087476 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 66, 66, 66, 39, 35, 35, 11, 35, 11, 11, 11, 1, 1, 1, 1, 11, 39, 39, 39, 39, 66, 66, 35, 11, 11, 1, 1, 1, 1, 1] 66 rigid atoms, others: [32, 33, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 246 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087476 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087476 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087476/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087476 Building REAL300004087477 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087477' /scratch/stefan/7774412/working/building/REAL300004087477 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087477 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087477/0 /scratch/stefan/7774412/working/building/REAL300004087477 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/601 `/scratch/stefan/7774412/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3=CC=CC=N3)N=C2)S1) `REAL300004087477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087477 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3=CC=CC=N3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 23, 23, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 11, 11, 11, 11, 21, 21, 7, 1, 9, 9, 9, 9, 1] 41 rigid atoms, others: [36, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087477 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3=CC=CC=N3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 11, 11, 4, 9, 27, 27, 27, 27, 27, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 27, 27, 27, 27, 11] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087477 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3=CC=CC=N3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 41, 41, 41, 27, 21, 21, 3, 21, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 41, 41, 21, 9, 1, 1, 1, 1, 9] 41 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 161 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087477 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087477 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087477/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087477 Building REAL300004087478 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087478' /scratch/stefan/7774412/working/building/REAL300004087478 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087478 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087478/0 /scratch/stefan/7774412/working/building/REAL300004087478 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/602 `/scratch/stefan/7774412/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1) `REAL300004087478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087478 none COC1=CC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [30, 13, 13, 23, 23, 13, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 23, 23, 23, 30, 30, 30, 23, 23, 13, 13, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23] 60 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087478 none COC1=CC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 39, 60, 60, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 1, 5, 5, 23, 39, 39, 23, 23, 23, 2, 2, 2, 1] 60 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 20, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087478 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087478 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087478/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087478 Building REAL300004087479 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087479' /scratch/stefan/7774412/working/building/REAL300004087479 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087479 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087479/0 /scratch/stefan/7774412/working/building/REAL300004087479 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/603 `/scratch/stefan/7774412/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C(F)F)=C2)S1) `REAL300004087479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087479 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [13, 14, 14, 14, 27, 37, 37, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 9, 9, 1, 14, 14, 14, 14, 27, 27, 11, 2, 2, 2, 9, 1] 41 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087479 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 28, 28, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 28, 14] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087479 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087479 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087479/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087479 Building REAL300004087480 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087480' /scratch/stefan/7774412/working/building/REAL300004087480 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087480 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087480/0 /scratch/stefan/7774412/working/building/REAL300004087480 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/604 `/scratch/stefan/7774412/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC2C2=CC=CC([N+](=O)[O-])=C2)S1) `REAL300004087480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087480 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC2C2=CC=CC([N+](=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 8, 13, 13, 5, 5, 5, 1, 5, 1, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 1, 1, 10, 10, 10, 10] 20 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 59 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087480 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC2C2=CC=CC([N+](=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 15, 15, 15, 15] 20 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087480 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC2C2=CC=CC([N+](=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 20, 20, 20, 15, 15, 15, 10, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 15, 15, 20, 20, 15, 10, 10, 10, 10, 1, 1, 1, 1] 20 rigid atoms, others: [35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087480 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087480 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087480/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087480 Building REAL300004087481 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087481' /scratch/stefan/7774412/working/building/REAL300004087481 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087481 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087481/0 /scratch/stefan/7774412/working/building/REAL300004087481 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/605 `/scratch/stefan/7774412/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(S(C)(=O)=O)C=C2)S1) `REAL300004087481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087481 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 11, 13, 13, 8, 8, 8, 6, 8, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8, 8, 8, 8, 11, 11, 8, 6, 6, 4, 4, 1, 1, 3, 3, 3, 1, 1] 15 rigid atoms, others: [35, 36, 40, 41, 13, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087481 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 6, 6, 8, 8, 6, 8, 11, 11, 11, 8, 8, 1, 2, 2, 2, 2, 2, 3, 6, 6, 6, 6, 8, 8, 11, 11, 11, 8, 8] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087481 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087481 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087481/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087481 Building REAL300004087482 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087482' /scratch/stefan/7774412/working/building/REAL300004087482 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087482 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087482/0 /scratch/stefan/7774412/working/building/REAL300004087482 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/606 `/scratch/stefan/7774412/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(CC(C)C)S2)S1) `REAL300004087482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087482 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(CC(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 34, 38, 38, 17, 11, 11, 1, 11, 1, 1, 1, 1, 1, 6, 10, 10, 1, 17, 18, 18, 18, 34, 34, 11, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10] 66 rigid atoms, others: [10, 12, 13, 14, 15, 16, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087482 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(CC(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 29, 35, 35, 17, 1, 2, 2, 2, 2, 2, 2, 17, 29, 29, 35, 35, 35, 35, 35, 35, 35] 66 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087482 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087482 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087482/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087482 Building REAL300004087483 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087483' /scratch/stefan/7774412/working/building/REAL300004087483 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087483 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087483/0 /scratch/stefan/7774412/working/building/REAL300004087483 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/607 `/scratch/stefan/7774412/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3CCCCC3)=C2)S1) `REAL300004087483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087483 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3CCCCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 29, 29, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 13, 13, 13, 13, 25, 25, 9, 1, 6, 6, 6, 6, 7, 6, 7, 6, 7, 6, 6, 1] 113 rigid atoms, others: [10, 12, 13, 14, 15, 16, 22, 42, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087483 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3CCCCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 61, 61, 61, 61, 61, 13, 1, 2, 2, 2, 2, 2, 2, 13, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 13] 113 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087483 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3CCCCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 113, 113, 113, 61, 37, 33, 6, 33, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 61, 61, 61, 61, 113, 113, 37, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 113 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 42]) total number of confs: 449 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087483 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087483 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087483/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087483 Building REAL300004087484 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087484' /scratch/stefan/7774412/working/building/REAL300004087484 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087484 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087484/0 /scratch/stefan/7774412/working/building/REAL300004087484 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/608 `/scratch/stefan/7774412/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)S1) `REAL300004087484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087484 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 13, 13, 13, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 43 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087484 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 45 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087484 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087484 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087484/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087484 Building REAL300004087485 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087485' /scratch/stefan/7774412/working/building/REAL300004087485 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087485 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087485/0 /scratch/stefan/7774412/working/building/REAL300004087485 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/609 `/scratch/stefan/7774412/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(CC(C)(C)C)S2)S1) `REAL300004087485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087485 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(CC(C)(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 18, 33, 44, 44, 18, 12, 12, 1, 12, 1, 1, 1, 1, 1, 5, 9, 9, 8, 1, 18, 18, 18, 18, 33, 33, 12, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9] 63 rigid atoms, others: [10, 12, 13, 14, 15, 16, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 205 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087485 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(CC(C)(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 35, 37, 37, 37, 18, 1, 2, 2, 2, 2, 2, 2, 18, 35, 35, 37, 37, 37, 37, 37, 37, 37, 37, 37] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087485 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087485 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087485/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087485 Building REAL300004087486 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087486' /scratch/stefan/7774412/working/building/REAL300004087486 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087486 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087486/0 /scratch/stefan/7774412/working/building/REAL300004087486 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/610 `/scratch/stefan/7774412/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CC3CC2C)S1) `REAL300004087486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087486 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CC3CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 15 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 38, 39, 37]) total number of confs: 65 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: REAL300004087486 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CC3CC2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087486 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087486 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087486/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087486 Building REAL300004087487 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087487' /scratch/stefan/7774412/working/building/REAL300004087487 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087487 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087487/0 /scratch/stefan/7774412/working/building/REAL300004087487 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/611 `/scratch/stefan/7774412/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087487 none CCCC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [44, 35, 17, 17, 17, 3, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 44, 44, 44, 44, 44, 35, 35, 17, 3, 17, 17, 2, 2, 2, 2, 2, 2] 63 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 208 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087487 none CCCC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 13, 17, 17, 17, 27, 39, 39, 17, 17, 17, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 13, 27, 27, 17, 17, 17] 63 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087487 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087487 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087487/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087487 Building REAL300004087488 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087488' /scratch/stefan/7774412/working/building/REAL300004087488 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087488 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087488/0 /scratch/stefan/7774412/working/building/REAL300004087488 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/612 `/scratch/stefan/7774412/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC12CCC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)(CC1)CC2) `REAL300004087488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087488 none COC12CCC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 3, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 7, 7, 7, 7, 8, 8, 8, 7, 7, 7, 7, 3, 2, 2, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 11 rigid atoms, others: [33, 34, 35, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087488 none COC12CCC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 11, 11, 11, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 5, 11, 11, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 30, 31, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087488 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087488/1 /scratch/stefan/7774412/working/building/REAL300004087488 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/613 `/scratch/stefan/7774412/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC12CCC(C(=O)[N-]C3=NC(CC(=O)[O-])=C(C)S3)(CC1)CC2) `REAL300004087488.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087488/1/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: REAL300004087488 none COC12CCC(C(=O)[N-]C3=NC(CC(=O)[O-])=C(C)S3)(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 55, 55, 134, 134, 55, 12, 55, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 134, 134, 134, 134, 154, 154, 154, 134, 134, 134, 134, 2, 2, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134] 201 rigid atoms, others: [32, 33, 34, 8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087488 none COC12CCC(C(=O)[N-]C3=NC(CC(=O)[O-])=C(C)S3)(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 6, 6, 37, 134, 134, 134, 187, 201, 201, 134, 134, 134, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 187, 187, 134, 134, 134, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 32, 34, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 30, 31]) total number of confs: 552 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087488 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087488 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087488/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087488/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087488 Building REAL300004087489 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087489' /scratch/stefan/7774412/working/building/REAL300004087489 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087489 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087489/0 /scratch/stefan/7774412/working/building/REAL300004087489 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/614 `/scratch/stefan/7774412/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1) `REAL300004087489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087489 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 30, 53, 53, 16, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 22, 22, 16, 16, 16, 16, 30, 30, 12, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 22] 122 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 267 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087489 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 16, 16, 16, 16, 16, 16, 16, 66, 66, 66, 66, 66, 81, 81, 1, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 66, 66, 81, 81, 81, 81, 81, 81, 81] 122 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 214 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087489 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 116, 121, 121, 66, 55, 43, 9, 43, 9, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 6, 66, 66, 66, 66, 116, 116, 55, 9, 9, 9, 9, 1, 1, 6, 6, 6, 6, 6, 6, 6] 122 rigid atoms, others: [38, 39, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 511 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087489 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087489/1 /scratch/stefan/7774412/working/building/REAL300004087489 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/615 `/scratch/stefan/7774412/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1) `REAL300004087489.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087489 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 149, 170, 170, 111, 48, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 111, 111, 111, 111, 149, 149, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 13, 13, 13] 201 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 503 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087489 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 13, 56, 56, 111, 111, 111, 111, 111, 111, 111, 159, 159, 159, 159, 159, 171, 171, 1, 2, 2, 2, 2, 2, 111, 111, 111, 111, 159, 159, 171, 171, 171, 171, 171, 171, 171] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 472 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087489 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=NN2C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 201, 201, 201, 159, 75, 26, 8, 26, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 4, 4, 159, 159, 159, 159, 201, 201, 8, 8, 8, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [37, 38, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 515 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087489 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087489 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087489/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087489/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087489 Building REAL300004087490 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087490' /scratch/stefan/7774412/working/building/REAL300004087490 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087490 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087490/0 /scratch/stefan/7774412/working/building/REAL300004087490 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/616 `/scratch/stefan/7774412/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NOC(C3CC3)=C2)S1) `REAL300004087490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087490 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NOC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 23, 30, 30, 15, 15, 15, 7, 15, 1, 1, 1, 1, 1, 1, 8, 8, 1, 15, 15, 15, 15, 23, 23, 15, 7, 7, 8, 8, 8, 8, 8, 1] 59 rigid atoms, others: [35, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 142 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087490 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NOC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 15, 15, 15, 15, 37, 37, 15, 1, 2, 2, 2, 2, 2, 2, 8, 8, 37, 37, 37, 37, 37, 15] 59 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087490 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NOC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 59, 59, 59, 37, 37, 37, 26, 37, 8, 8, 8, 8, 1, 1, 1, 1, 8, 37, 37, 37, 37, 59, 59, 37, 26, 26, 1, 1, 1, 1, 1, 8] 59 rigid atoms, others: [32, 33, 34, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 255 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087490 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087490/1 /scratch/stefan/7774412/working/building/REAL300004087490 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/617 `/scratch/stefan/7774412/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NOC(C3CC3)=C2)S1) `REAL300004087490.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087490/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087490 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NOC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 96, 111, 111, 83, 46, 22, 5, 22, 1, 1, 1, 1, 1, 1, 10, 10, 1, 83, 83, 83, 83, 96, 96, 5, 5, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087490 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NOC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 12, 28, 28, 64, 83, 83, 83, 83, 195, 195, 83, 1, 2, 2, 2, 3, 3, 64, 64, 195, 195, 195, 195, 195, 83] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087490 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NOC(C3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 12, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 195, 201, 201, 201, 195, 140, 91, 33, 91, 10, 10, 10, 10, 1, 1, 1, 1, 10, 195, 195, 195, 195, 201, 201, 33, 33, 1, 1, 1, 1, 1, 10] 201 rigid atoms, others: [32, 33, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 490 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087490 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087490 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087490/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087490/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087490 Building REAL300004087491 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087491' /scratch/stefan/7774412/working/building/REAL300004087491 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087491 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087491/0 /scratch/stefan/7774412/working/building/REAL300004087491 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/618 `/scratch/stefan/7774412/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2)S1) `REAL300004087491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087491 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 39 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087491 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 11, 11, 17, 17, 11, 17, 17, 1, 2, 2, 2, 2, 2, 2, 11, 11, 17, 17, 11, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087491 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087491 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087491/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087491 Building REAL300004087492 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087492' /scratch/stefan/7774412/working/building/REAL300004087492 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087492 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087492/0 /scratch/stefan/7774412/working/building/REAL300004087492 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/619 `/scratch/stefan/7774412/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2Cl)S1) `REAL300004087492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087492 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 43, 43, 43, 28, 28, 24, 9, 27, 9, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 43, 43, 27, 9, 9, 1, 1, 1, 1] 43 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 173 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087492 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 13, 13, 28, 28, 13, 28, 28, 28, 1, 2, 2, 2, 2, 2, 2, 13, 13, 28, 28, 25, 28] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087492 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087492 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087492/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087492 Building REAL300004087493 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087493' /scratch/stefan/7774412/working/building/REAL300004087493 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087493 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087493/0 /scratch/stefan/7774412/working/building/REAL300004087493 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/620 `/scratch/stefan/7774412/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(F)=C2)S1) `REAL300004087493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087493 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 23, 23, 23, 16, 16, 16, 5, 16, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 23, 23, 16, 5, 5, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087493 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 7, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 7, 7, 16, 16, 16, 16] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087493 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087493 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087493/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087493 Building REAL300004087494 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087494' /scratch/stefan/7774412/working/building/REAL300004087494 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087494 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087494/0 /scratch/stefan/7774412/working/building/REAL300004087494 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/621 `/scratch/stefan/7774412/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(Br)O2)S1) `REAL300004087494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087494 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(Br)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 31, 31, 31, 26, 26, 26, 11, 25, 10, 1, 1, 1, 1, 1, 1, 1, 25, 26, 26, 26, 31, 31, 26, 11, 10, 1, 1] 31 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087494 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(Br)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 11, 11, 25, 25, 25, 26, 26, 1, 2, 2, 2, 2, 2, 2, 11, 11, 26, 26] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087494 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087494 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087494/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087494 Building REAL300004087495 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087495' /scratch/stefan/7774412/working/building/REAL300004087495 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087495 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087495/0 /scratch/stefan/7774412/working/building/REAL300004087495 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/622 `/scratch/stefan/7774412/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SC=NC3=C2)S1) `REAL300004087495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087495 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SC=NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087495 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SC=NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087495 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087495 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087495/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087495 Building REAL300004087496 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087496' /scratch/stefan/7774412/working/building/REAL300004087496 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087496 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087496/0 /scratch/stefan/7774412/working/building/REAL300004087496 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/623 `/scratch/stefan/7774412/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087496 none CSC1=CC=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 18, 23, 23, 13, 9, 3, 3, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 23, 23, 31, 31, 31, 23, 23, 13, 13, 9, 9, 3, 2, 2, 2, 2, 2, 23, 23] 41 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087496 none CSC1=CC=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 7, 9, 21, 21, 23, 23, 23, 23, 33, 33, 33, 23, 23, 23, 1, 1, 6, 6, 6, 1, 1, 7, 7, 9, 9, 23, 33, 33, 23, 23, 23, 1, 1] 41 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 38, 21, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087496 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087496 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087496/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087496 Building REAL300004087497 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087497' /scratch/stefan/7774412/working/building/REAL300004087497 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087497 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087497/0 /scratch/stefan/7774412/working/building/REAL300004087497 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/624 `/scratch/stefan/7774412/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C([N+](=O)[O-])N1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087497 none CC1=NC=C([N+](=O)[O-])N1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 11, 11, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 4, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 5, 5, 5, 5, 4, 4, 2, 3, 3, 2, 2, 2] 9 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087497 none CC1=NC=C([N+](=O)[O-])N1CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 11, 11, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 4, 4, 5, 5, 5, 5, 9, 9, 9, 5, 5, 5, 2, 2, 2, 1, 2, 2, 5, 9, 9, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 26] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087497 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087497/1 /scratch/stefan/7774412/working/building/REAL300004087497 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/625 `/scratch/stefan/7774412/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C([N+](=O)[O-])N1CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087497.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087497/1/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: REAL300004087497 none CC1=NC=C([N+](=O)[O-])N1CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 11, 11, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 162, 162, 162, 134, 50, 12, 50, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 162, 162, 162, 162, 134, 134, 2, 2, 2, 2, 2] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087497 none CC1=NC=C([N+](=O)[O-])N1CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 11, 11, 8, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 4, 18, 18, 55, 162, 162, 162, 201, 201, 201, 162, 162, 162, 2, 2, 2, 1, 4, 4, 201, 201, 162, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 26] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 487 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087497 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087497 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087497/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087497/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087497 Building REAL300004087498 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087498' /scratch/stefan/7774412/working/building/REAL300004087498 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087498 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087498/0 /scratch/stefan/7774412/working/building/REAL300004087498 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/626 `/scratch/stefan/7774412/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(P(C)(C)=O)C=C2)S1) `REAL300004087498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087498 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(P(C)(C)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'P.3', 'C.3', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 13, 5, 5, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 9, 9, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 1, 1, 4, 4, 4, 4, 7, 7, 4, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 19 rigid atoms, others: [37, 38, 10, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087498 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(P(C)(C)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'P.3', 'C.3', 'C.3', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 13, 5, 5, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 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 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 4, 3, 2, 13, 13, 13, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 13, 13, 13, 13, 13, 13, 4, 4] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087498 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087498 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087498/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087498 Building REAL300004087499 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087499' /scratch/stefan/7774412/working/building/REAL300004087499 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087499 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087499/0 /scratch/stefan/7774412/working/building/REAL300004087499 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/627 `/scratch/stefan/7774412/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(=O)NC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087499 none COC1=CC(=O)NC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 15, 15, 15, 15, 15, 15, 15, 4, 2, 4, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 19, 19, 19, 15, 15, 15, 2, 2, 2, 2, 2, 2] 33 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087499 none COC1=CC(=O)NC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 15, 15, 15, 27, 33, 33, 15, 15, 15, 4, 4, 4, 1, 1, 1, 12, 27, 27, 15, 15, 15] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087499 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087499/1 /scratch/stefan/7774412/working/building/REAL300004087499 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/628 `/scratch/stefan/7774412/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(=O)NC=C1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087499.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087499/1/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: REAL300004087499 none COC1=CC(=O)NC=C1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 116, 116, 116, 116, 116, 116, 116, 60, 13, 60, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 153, 153, 153, 116, 116, 116, 2, 2, 2, 2, 2] 201 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 328 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087499 none COC1=CC(=O)NC=C1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 35, 116, 116, 116, 163, 179, 179, 116, 116, 116, 3, 3, 3, 1, 1, 1, 163, 163, 116, 116, 116] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087499 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087499 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087499/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087499/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087499 Building REAL300004087500 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087500' /scratch/stefan/7774412/working/building/REAL300004087500 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087500 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087500/0 /scratch/stefan/7774412/working/building/REAL300004087500 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/629 `/scratch/stefan/7774412/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3C=CC=C3)=CC=C2Cl)S1) `REAL300004087500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087500 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3C=CC=C3)=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 1, 2, 2, 2, 2, 1, 1] 5 rigid atoms, others: [36, 37, 10, 12, 13, 14, 15, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087500 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3C=CC=C3)=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087500 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(N3C=CC=C3)=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 3, 3] 5 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 15 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087500 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087500 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087500/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087500 Building REAL300004087501 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087501' /scratch/stefan/7774412/working/building/REAL300004087501 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087501 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087501/0 /scratch/stefan/7774412/working/building/REAL300004087501 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/630 `/scratch/stefan/7774412/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCS(=O)(=O)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087501 none CCCCS(=O)(=O)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [44, 30, 28, 14, 6, 14, 14, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 44, 44, 44, 44, 44, 30, 30, 28, 28, 6, 6, 2, 2, 2, 2, 2, 2] 67 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087501 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087501/1 /scratch/stefan/7774412/working/building/REAL300004087501 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/631 `/scratch/stefan/7774412/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCS(=O)(=O)CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087501.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087501 none CCCCS(=O)(=O)CC(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 11, 11, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 163, 162, 153, 123, 153, 153, 63, 12, 63, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 164, 164, 164, 164, 164, 163, 163, 162, 162, 123, 123, 2, 2, 2, 2, 2] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 704 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087501 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087501 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087501/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087501/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087501 Building REAL300004087502 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087502' /scratch/stefan/7774412/working/building/REAL300004087502 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087502 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087502/0 /scratch/stefan/7774412/working/building/REAL300004087502 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/632 `/scratch/stefan/7774412/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCCCCC2)S1) `REAL300004087502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087502 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 13, 13, 13, 11, 11, 11, 9, 11, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 13, 13, 11, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087502 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 4, 8, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 3, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087502 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087502/1 /scratch/stefan/7774412/working/building/REAL300004087502 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/633 `/scratch/stefan/7774412/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCCCCC2)S1) `REAL300004087502.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087502/1/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: REAL300004087502 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 201, 201, 201, 179, 100, 52, 15, 52, 7, 1, 1, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087502 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 38, 38, 89, 156, 179, 179, 179, 179, 179, 179, 1, 2, 2, 2, 2, 2, 89, 89, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179, 179] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087502 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087502 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087502/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087502/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087502 Building REAL300004087503 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087503' /scratch/stefan/7774412/working/building/REAL300004087503 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087503 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087503/0 /scratch/stefan/7774412/working/building/REAL300004087503 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/634 `/scratch/stefan/7774412/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)S1) `REAL300004087503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087503 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087503 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087503 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087503 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087503/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087503 Building REAL300004087504 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087504' /scratch/stefan/7774412/working/building/REAL300004087504 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087504 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087504/0 /scratch/stefan/7774412/working/building/REAL300004087504 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/635 `/scratch/stefan/7774412/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCCC1) `REAL300004087504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087504 none COC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 3, 3, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 11, 11, 11, 11, 12, 12, 12, 3, 2, 2, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 28, 29, 30] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087504 none COC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 8, 8, 8, 11, 11, 11, 18, 18, 18, 11, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 18, 18, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 40, 41, 42, 39, 34, 16, 17, 18, 19, 20, 21, 38, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087504 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087504/1 /scratch/stefan/7774412/working/building/REAL300004087504 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/636 `/scratch/stefan/7774412/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCCCC1) `REAL300004087504.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087504/1/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: REAL300004087504 none COC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 154, 59, 12, 59, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 154, 154, 154, 154, 154, 154, 158, 158, 158, 2, 2, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15, 27, 28, 29] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087504 none COC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 10, 10, 52, 154, 154, 154, 201, 201, 201, 154, 154, 154, 1, 1, 1, 1, 1, 1, 5, 5, 5, 201, 201, 154, 154, 154, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 40, 41, 39, 34, 16, 17, 18, 19, 20, 21, 38, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 502 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087504 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087504 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087504/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087504/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087504 Building REAL300004087505 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087505' /scratch/stefan/7774412/working/building/REAL300004087505 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087505 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087505/0 /scratch/stefan/7774412/working/building/REAL300004087505 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/637 `/scratch/stefan/7774412/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2CCCCC3)S1) `REAL300004087505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087505 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2CCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 19, 19, 19, 12, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 73 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087505 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC3=C2CCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 12, 12, 11, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087505 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087505 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087505/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087505 Building REAL300004087506 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087506' /scratch/stefan/7774412/working/building/REAL300004087506 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087506 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087506/0 /scratch/stefan/7774412/working/building/REAL300004087506 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/638 `/scratch/stefan/7774412/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN(CC(F)(F)F)C=C2)S1) `REAL300004087506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087506 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN(CC(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 86, 131, 131, 50, 46, 44, 8, 44, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 50, 50, 50, 50, 86, 86, 46, 8, 8, 9, 9, 1, 1] 194 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087506 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=NN(CC(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 21, 50, 50, 50, 125, 125, 125, 125, 50, 50, 1, 2, 2, 2, 2, 2, 2, 21, 21, 125, 125, 50, 50] 194 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087506 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087506/1 /scratch/stefan/7774412/working/building/REAL300004087506 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/639 `/scratch/stefan/7774412/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN(CC(F)(F)F)C=C2)S1) `REAL300004087506.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087506/1/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: REAL300004087506 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN(CC(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [114, 114, 114, 114, 146, 154, 154, 114, 67, 29, 6, 29, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 114, 114, 114, 114, 146, 146, 6, 6, 7, 7, 1, 1] 201 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 453 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087506 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CC2=NN(CC(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 3, 5, 5, 1, 1, 1, 12, 38, 38, 86, 114, 114, 114, 165, 165, 165, 165, 114, 114, 1, 2, 2, 2, 3, 3, 86, 86, 165, 165, 114, 114] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 661 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087506 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087506 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087506/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087506/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087506 Building REAL300004087507 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087507' /scratch/stefan/7774412/working/building/REAL300004087507 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087507 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087507/0 /scratch/stefan/7774412/working/building/REAL300004087507 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/640 `/scratch/stefan/7774412/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CCC2)S1) `REAL300004087507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087507 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 27, 29, 29, 15, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 27, 27, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 41 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087507 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 14, 15, 15, 15, 22, 22, 22, 1, 2, 2, 2, 2, 2, 2, 15, 15, 14, 15, 22, 22, 22, 22, 22, 22, 22] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 79 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087507 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 41, 41, 41, 22, 18, 18, 5, 18, 5, 5, 4, 5, 5, 1, 1, 1, 1, 1, 22, 22, 22, 22, 41, 41, 18, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 165 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087507 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087507 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087507/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087507 Building REAL300004087508 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087508' /scratch/stefan/7774412/working/building/REAL300004087508 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087508 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087508/0 /scratch/stefan/7774412/working/building/REAL300004087508 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/641 `/scratch/stefan/7774412/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC=C2)S1) `REAL300004087508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087508 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 9, 9, 9, 9, 17, 17, 9, 1, 1, 1, 1, 3, 3, 3, 3] 17 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087508 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087508 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 9, 7, 3, 7, 3, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 3, 2, 3, 3, 1, 1, 1, 1] 17 rigid atoms, others: [34, 35, 36, 37, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087508 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087508 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087508/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087508 Building REAL300004087509 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087509' /scratch/stefan/7774412/working/building/REAL300004087509 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087509 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087509/0 /scratch/stefan/7774412/working/building/REAL300004087509 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/642 `/scratch/stefan/7774412/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2CCOCC2)S1) `REAL300004087509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087509 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 26, 26, 14, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 14, 14, 26, 26, 11, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2] 26 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087509 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 47 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087509 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 26, 26, 26, 15, 12, 10, 2, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 26, 26, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 101 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087509 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087509 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087509/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087509 Building REAL300004087510 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087510' /scratch/stefan/7774412/working/building/REAL300004087510 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087510 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087510/0 /scratch/stefan/7774412/working/building/REAL300004087510 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/643 `/scratch/stefan/7774412/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2C=C1) `REAL300004087510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087510 none CCOC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7] 17 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 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: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087510 none CCOC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 11, 11, 11, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 7, 7, 7, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [2, 3, 4, 5, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24, 25, 37] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087510 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087510 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087510/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087510 Building REAL300004087511 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087511' /scratch/stefan/7774412/working/building/REAL300004087511 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087511 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087511/0 /scratch/stefan/7774412/working/building/REAL300004087511 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/644 `/scratch/stefan/7774412/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C(F)C2=CC=CC=C2)S1) `REAL300004087511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087511 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C(F)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 77, 77, 77, 41, 28, 28, 11, 28, 2, 11, 11, 1, 2, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 77, 77, 28, 11, 11, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1] 77 rigid atoms, others: [37, 38, 39, 40, 41, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 329 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087511 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C(F)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 12, 12, 12, 41, 41, 41, 41, 41, 41, 41, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 41, 41, 41, 41, 41, 41] 77 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087511 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087511/1 /scratch/stefan/7774412/working/building/REAL300004087511 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/645 `/scratch/stefan/7774412/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C(F)C2=CC=CC=C2)S1) `REAL300004087511.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087511/1/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: REAL300004087511 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C(F)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 201, 201, 201, 156, 57, 17, 5, 17, 2, 5, 5, 1, 2, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 201, 201, 5, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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: REAL300004087511 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C(F)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 15, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 58, 58, 124, 124, 124, 156, 156, 156, 156, 156, 156, 156, 1, 2, 2, 2, 2, 2, 124, 124, 124, 124, 124, 124, 156, 156, 156, 156, 156, 156] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087511 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087511 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087511/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087511/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087511 Building REAL300004087512 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087512' /scratch/stefan/7774412/working/building/REAL300004087512 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087512 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087512/0 /scratch/stefan/7774412/working/building/REAL300004087512 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/646 `/scratch/stefan/7774412/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3)C=C2)S1) `REAL300004087512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087512 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 17, 17, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 36 rigid atoms, others: [38, 39, 10, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 75 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087512 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 3, 5, 19, 19, 19, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 19, 19, 19, 19, 19, 19, 19, 7, 7] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087512 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 36, 36, 36, 19, 15, 13, 4, 13, 3, 5, 5, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 36, 36, 15, 5, 5, 2, 2, 2, 1, 1, 1, 1, 5, 5] 36 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 162 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087512 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087512 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087512/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087512 Building REAL300004087513 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087513' /scratch/stefan/7774412/working/building/REAL300004087513 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087513 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087513/0 /scratch/stefan/7774412/working/building/REAL300004087513 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/647 `/scratch/stefan/7774412/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC(C)C)S2)S1) `REAL300004087513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087513 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 23, 43, 44, 44, 22, 14, 12, 1, 12, 1, 1, 1, 1, 1, 5, 7, 7, 1, 22, 23, 23, 23, 43, 43, 15, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7] 72 rigid atoms, others: [10, 12, 13, 14, 15, 16, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087513 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC(C)C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 22, 22, 22, 22, 34, 39, 39, 22, 1, 2, 2, 2, 2, 2, 2, 22, 22, 34, 34, 39, 39, 39, 39, 39, 39, 39] 72 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087513 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087513 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087513/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087513 Building REAL300004087514 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087514' /scratch/stefan/7774412/working/building/REAL300004087514 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087514 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087514/0 /scratch/stefan/7774412/working/building/REAL300004087514 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/648 `/scratch/stefan/7774412/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C3OCCCC3=C2)S1) `REAL300004087514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087514 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C3OCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 47, 48, 48, 27, 27, 25, 13, 25, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 28, 28, 28, 47, 47, 27, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 228 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087514 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C3OCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 2, 2, 2, 8, 8, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27] 48 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087514 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087514 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087514/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087514 Building REAL300004087515 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087515' /scratch/stefan/7774412/working/building/REAL300004087515 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087515 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087515/0 /scratch/stefan/7774412/working/building/REAL300004087515 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/649 `/scratch/stefan/7774412/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087515 none CC1=NN(C2=CC=CC=C2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 27, 39, 39, 39, 63, 63, 63, 39, 39, 39, 6, 6, 6, 6, 1, 1, 1, 1, 1, 27, 63, 63, 39, 39, 39, 6] 63 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087515 none CC1=NN(C2=CC=CC=C2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 1, 6, 6, 1, 1, 12, 12, 14, 25, 25, 25, 49, 59, 59, 25, 25, 25, 1, 2, 2, 2, 6, 6, 1, 6, 6, 14, 49, 49, 25, 25, 25, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 24, 39] set([5, 6, 7, 8, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087515 none CC1=NN(C2=CC=CC=C2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 25, 25, 25, 25, 39, 39, 29, 39, 39, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 25, 25, 25, 25, 39, 39, 29, 39, 39, 2, 2, 2, 2, 2, 2, 25] 63 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087515 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087515 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087515/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087515 Building REAL300004087516 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087516' /scratch/stefan/7774412/working/building/REAL300004087516 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087516 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087516/0 /scratch/stefan/7774412/working/building/REAL300004087516 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/650 `/scratch/stefan/7774412/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(=O)C3=CC=CC=C3)=CN2)S1) `REAL300004087516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087516 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(=O)C3=CC=CC=C3)=CN2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 38, 52, 52, 22, 16, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 22, 23, 23, 23, 38, 38, 16, 1, 7, 7, 7, 7, 7, 1, 1] 116 rigid atoms, others: [32, 38, 39, 10, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 225 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087516 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(=O)C3=CC=CC=C3)=CN2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 72, 72, 72, 72, 72, 72, 72, 22, 22, 1, 2, 2, 2, 2, 2, 2, 22, 72, 72, 72, 72, 72, 22, 22] 116 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 191 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087516 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(=O)C3=CC=CC=C3)=CN2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 116, 116, 116, 72, 54, 44, 7, 44, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 72, 72, 72, 72, 116, 116, 54, 7, 1, 1, 1, 1, 1, 7, 7] 116 rigid atoms, others: [33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 437 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087516 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087516 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087516/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087516 Building REAL300004087517 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087517' /scratch/stefan/7774412/working/building/REAL300004087517 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087517 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087517/0 /scratch/stefan/7774412/working/building/REAL300004087517 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/651 `/scratch/stefan/7774412/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=NN2C)S1) `REAL300004087517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087517 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 35, 43, 43, 19, 14, 12, 1, 12, 1, 1, 1, 1, 7, 7, 1, 2, 7, 7, 1, 1, 1, 19, 19, 19, 19, 35, 35, 14, 1, 7, 7, 7, 7, 2, 2, 2] 67 rigid atoms, others: [32, 10, 12, 13, 14, 15, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 194 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087517 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 19, 19, 19, 39, 39, 19, 36, 39, 39, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 19, 39, 39, 39, 39, 19, 19, 19] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087517 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 67, 67, 67, 39, 29, 26, 7, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 39, 39, 67, 67, 29, 7, 1, 1, 1, 1, 7, 7, 7] 67 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087517 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087517 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087517/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087517 Building REAL300004087518 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087518' /scratch/stefan/7774412/working/building/REAL300004087518 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087518 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087518/0 /scratch/stefan/7774412/working/building/REAL300004087518 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/652 `/scratch/stefan/7774412/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3CC3)C=C2)S1) `REAL300004087518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087518 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 13, 22, 22, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 11, 22, 22, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 22, 22, 22, 22, 22, 1, 1] 78 rigid atoms, others: [36, 37, 10, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 126 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087518 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 3, 3, 31, 48, 48, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 48, 48, 48, 48, 48, 7, 7] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087518 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 78, 78, 78, 48, 37, 34, 19, 34, 19, 22, 22, 11, 1, 1, 1, 1, 22, 22, 48, 48, 48, 48, 78, 78, 37, 22, 22, 1, 1, 1, 1, 1, 22, 22] 78 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37]) total number of confs: 296 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087518 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087518 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087518/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087518 Building REAL300004087519 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087519' /scratch/stefan/7774412/working/building/REAL300004087519 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087519 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087519/0 /scratch/stefan/7774412/working/building/REAL300004087519 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/653 `/scratch/stefan/7774412/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=CC3=NC=NC=C32)S1) `REAL300004087519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087519 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=CC3=NC=NC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 16, 16, 16, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 7, 1, 1, 1, 1] 16 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087519 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=CC3=NC=NC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087519 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087519 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087519/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087519 Building REAL300004087520 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087520' /scratch/stefan/7774412/working/building/REAL300004087520 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087520 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087520/0 /scratch/stefan/7774412/working/building/REAL300004087520 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/654 `/scratch/stefan/7774412/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC(C3=CC=CC=C3)C2)S1) `REAL300004087520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087520 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 38, 73, 73, 21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 21, 21, 21, 21, 38, 38, 12, 6, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 219 rigid atoms, others: [32, 33, 39, 40, 10, 12, 13, 14, 15, 16, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38]) total number of confs: 290 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087520 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 21, 21, 21, 21, 40, 40, 21, 40, 40, 21, 1, 2, 2, 2, 2, 2, 3, 63, 21, 21, 21, 40, 40, 40, 40, 40, 21, 21] 219 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 249 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087520 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(O)CC(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 219 conformations in input total number of sets (complete confs): 219 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 73, 73, 73, 40, 26, 26, 4, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 40, 40, 40, 40, 73, 73, 26, 12, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4] 219 rigid atoms, others: [34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 297 number of broken/clashed sets: 114 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087520 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087520/1 /scratch/stefan/7774412/working/building/REAL300004087520 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/655 `/scratch/stefan/7774412/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC(C3=CC=CC=C3)C2)S1) `REAL300004087520.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087520 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 513 conformations in input total number of sets (complete confs): 513 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 129, 171, 171, 93, 30, 9, 1, 9, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 93, 93, 93, 93, 129, 129, 6, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1] 513 rigid atoms, others: [32, 38, 39, 10, 12, 13, 14, 15, 16, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37]) total number of confs: 520 number of broken/clashed sets: 165 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087520 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 513 conformations in input total number of sets (complete confs): 513 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 50, 50, 93, 93, 93, 93, 126, 126, 93, 126, 126, 93, 1, 2, 2, 2, 2, 2, 279, 93, 93, 93, 126, 126, 126, 126, 126, 93, 93] 513 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 778 number of broken/clashed sets: 165 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087520 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(O)CC(C3=CC=CC=C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 513 conformations in input total number of sets (complete confs): 513 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 171, 171, 171, 126, 46, 17, 4, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 126, 126, 126, 126, 171, 171, 12, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4] 513 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 471 number of broken/clashed sets: 165 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087520 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087520 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087520/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087520/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087520 Building REAL300004087521 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087521' /scratch/stefan/7774412/working/building/REAL300004087521 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087521 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087521/0 /scratch/stefan/7774412/working/building/REAL300004087521 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/656 `/scratch/stefan/7774412/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Cl)C=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087521 none COC1=C(Cl)C=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 12, 12, 12, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 14, 14, 14, 12, 12, 12, 2, 2, 2, 2, 2, 2] 25 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087521 none COC1=C(Cl)C=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 16, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 12, 12, 12, 21, 21, 21, 12, 12, 12, 3, 3, 3, 1, 1, 1, 10, 21, 21, 12, 12, 12] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087521 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087521 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087521/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087521 Building REAL300004087522 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087522' /scratch/stefan/7774412/working/building/REAL300004087522 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087522 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087522/0 /scratch/stefan/7774412/working/building/REAL300004087522 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/657 `/scratch/stefan/7774412/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)NC(C(C)C)=C2)S1) `REAL300004087522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087522 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)NC(C(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 23, 43, 54, 54, 22, 13, 11, 1, 11, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 1, 22, 23, 23, 23, 43, 43, 14, 2, 2, 2, 2, 3, 3, 3, 1, 5, 5, 5, 5, 5, 5, 5, 1] 81 rigid atoms, others: [37, 10, 12, 13, 14, 45, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 248 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087522 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)NC(C(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 23, 27, 27, 22, 22, 23, 48, 48, 22, 1, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 22, 48, 48, 48, 48, 48, 48, 48, 23] 81 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 216 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087522 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087522 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087522/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087522 Building REAL300004087523 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087523' /scratch/stefan/7774412/working/building/REAL300004087523 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087523 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087523/0 /scratch/stefan/7774412/working/building/REAL300004087523 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/658 `/scratch/stefan/7774412/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOC1=CC=C2NC=C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C2=C1) `REAL300004087523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087523 none CCCOC1=CC=C2NC=C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 127, 87, 41, 41, 41, 41, 41, 41, 41, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 41, 41, 129, 129, 129, 129, 129, 127, 127, 41, 41, 41, 41, 15, 15, 2, 2, 2, 2, 2, 2, 41] 201 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 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: 388 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087523 none CCCOC1=CC=C2NC=C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 39, 39, 39, 41, 41, 41, 73, 87, 87, 41, 41, 41, 1, 1, 25, 25, 25, 25, 25, 20, 20, 1, 1, 1, 1, 7, 7, 39, 73, 73, 41, 41, 41, 1] 201 rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 46, 35, 25, 26, 37, 36] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 428 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087523 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087523 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087523/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087523 Building REAL300004087524 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087524' /scratch/stefan/7774412/working/building/REAL300004087524 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087524 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087524/0 /scratch/stefan/7774412/working/building/REAL300004087524 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/659 `/scratch/stefan/7774412/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C2CCCCN12) `REAL300004087524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087524 none CC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C2CCCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 13, 13, 13, 12, 12, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 12] 22 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087524 none CC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C2CCCCN12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 22, 22, 22, 12, 12, 12, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 22, 22, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 33, 35, 32, 39, 34, 17, 18, 19, 20, 21, 22, 36, 38, 37] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087524 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087524 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087524/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087524 Building REAL300004087525 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087525' /scratch/stefan/7774412/working/building/REAL300004087525 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087525 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087525/0 /scratch/stefan/7774412/working/building/REAL300004087525 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/660 `/scratch/stefan/7774412/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C(F)(F)F)O1) `REAL300004087525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087525 none CC1=C(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2] 13 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087525 none CC1=C(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C(F)(F)F)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 15, 15, 15, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 7, 13, 13, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 18, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087525 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087525 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087525/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087525 Building REAL300004087526 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087526' /scratch/stefan/7774412/working/building/REAL300004087526 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087526 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087526/0 /scratch/stefan/7774412/working/building/REAL300004087526 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/661 `/scratch/stefan/7774412/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3CCOCC3=C2)S1) `REAL300004087526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087526 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3CCOCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 12, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 24, 24, 24, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087526 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3CCOCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 12, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087526 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087526 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087526/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087526 Building REAL300004087527 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087527' /scratch/stefan/7774412/working/building/REAL300004087527 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087527 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087527/0 /scratch/stefan/7774412/working/building/REAL300004087527 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/662 `/scratch/stefan/7774412/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2=CC=CC=C2)C2CC2)S1) `REAL300004087527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087527 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2=CC=CC=C2)C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 30, 30, 30, 17, 11, 11, 5, 11, 2, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 17, 17, 17, 17, 30, 30, 11, 5, 2, 2, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 30 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087527 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2=CC=CC=C2)C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 13, 15, 15, 1, 2, 2, 2, 2, 2, 2, 13, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087527 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2=CC=CC=C2)C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 26, 28, 28, 15, 9, 9, 3, 9, 1, 3, 6, 6, 6, 6, 6, 6, 1, 1, 1, 15, 15, 15, 15, 26, 26, 9, 3, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 30 rigid atoms, others: [38, 39, 40, 41, 42, 12, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087527 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087527 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087527/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087527 Building REAL300004087528 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087528' /scratch/stefan/7774412/working/building/REAL300004087528 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087528 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087528/0 /scratch/stefan/7774412/working/building/REAL300004087528 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/663 `/scratch/stefan/7774412/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC=C2C2=CC=CC=C2)S1) `REAL300004087528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087528 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 15, 15, 7, 7, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 2, 4, 4, 7, 7, 7, 7, 11, 11, 7, 5, 5, 1, 1, 4, 4, 2, 4, 4] 15 rigid atoms, others: [33, 34, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087528 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 7, 7, 7, 7, 7, 15, 15, 11, 15, 15, 1, 2, 2, 2, 2, 2, 2, 4, 4, 7, 7, 15, 15, 11, 15, 15] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087528 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 15, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 13, 13, 4, 4, 1, 1, 1, 1, 1] 15 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 49 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087528 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087528/1 /scratch/stefan/7774412/working/building/REAL300004087528 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/664 `/scratch/stefan/7774412/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC=C2C2=CC=CC=C2)S1) `REAL300004087528.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087528/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087528 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 174, 201, 201, 127, 45, 23, 7, 23, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 127, 127, 127, 127, 174, 174, 7, 7, 1, 1, 4, 4, 1, 4, 4] 201 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 604 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087528 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 37, 37, 78, 127, 127, 127, 127, 127, 163, 163, 127, 163, 163, 1, 2, 2, 2, 3, 3, 78, 78, 127, 127, 163, 163, 127, 163, 162] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 570 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087528 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 84, 44, 15, 44, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 201, 201, 15, 15, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 523 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087528 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087528 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087528/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087528/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087528 Building REAL300004087529 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087529' /scratch/stefan/7774412/working/building/REAL300004087529 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087529 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087529/0 /scratch/stefan/7774412/working/building/REAL300004087529 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/665 `/scratch/stefan/7774412/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCC3CC3C2)S1) `REAL300004087529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087529 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCC3CC3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 13, 12, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087529 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCC3CC3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087529 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087529 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087529/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087529 Building REAL300004087530 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087530' /scratch/stefan/7774412/working/building/REAL300004087530 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087530 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087530/0 /scratch/stefan/7774412/working/building/REAL300004087530 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/666 `/scratch/stefan/7774412/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CN=C3)=N2)S1) `REAL300004087530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087530 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CN=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [15, 16, 16, 16, 29, 39, 39, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 5, 5, 4, 5, 5, 1, 16, 16, 16, 16, 29, 29, 11, 1, 5, 5, 4, 5] 47 rigid atoms, others: [10, 12, 13, 14, 15, 16, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) 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: REAL300004087530 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CN=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 29, 29, 29, 29, 29, 16, 1, 2, 2, 2, 2, 2, 2, 16, 29, 29, 29, 29] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087530 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(C3=CC=CN=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 47, 47, 47, 29, 23, 23, 5, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 29, 47, 47, 23, 5, 1, 1, 1, 1] 47 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 170 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087530 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087530 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087530/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087530 Building REAL300004087531 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087531' /scratch/stefan/7774412/working/building/REAL300004087531 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087531 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087531/0 /scratch/stefan/7774412/working/building/REAL300004087531 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/667 `/scratch/stefan/7774412/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3F)OC=N2)S1) `REAL300004087531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087531 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3F)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 48, 64, 64, 27, 17, 13, 1, 13, 1, 1, 1, 9, 9, 2, 9, 9, 9, 1, 1, 1, 27, 27, 27, 27, 48, 48, 17, 9, 9, 7, 9, 1] 135 rigid atoms, others: [35, 10, 12, 13, 14, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 280 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087531 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3F)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 27, 27, 83, 83, 71, 83, 83, 83, 27, 27, 27, 1, 2, 2, 2, 2, 2, 2, 83, 83, 83, 83, 27] 135 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087531 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3=CC=CC=C3F)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 135, 135, 135, 83, 66, 52, 9, 52, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 83, 83, 83, 83, 135, 135, 66, 1, 1, 1, 1, 9] 135 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 512 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087531 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087531 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087531/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087531 Building REAL300004087532 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087532' /scratch/stefan/7774412/working/building/REAL300004087532 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087532 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087532/0 /scratch/stefan/7774412/working/building/REAL300004087532 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/668 `/scratch/stefan/7774412/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)NC=C2)S1) `REAL300004087532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087532 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 35, 35, 35, 18, 14, 10, 1, 10, 1, 1, 1, 2, 2, 1, 1, 1, 18, 18, 18, 18, 35, 35, 14, 2, 3, 3, 3, 3, 3, 3, 1, 1, 1] 35 rigid atoms, others: [34, 35, 36, 10, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087532 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087532 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087532 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087532/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087532 Building REAL300004087533 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087533' /scratch/stefan/7774412/working/building/REAL300004087533 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087533 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087533/0 /scratch/stefan/7774412/working/building/REAL300004087533 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/669 `/scratch/stefan/7774412/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC3=CC(C)=CN=C32)S1) `REAL300004087533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087533 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC3=CC(C)=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 5, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 33, 33, 33, 21, 21, 20, 6, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 33, 33, 21, 6, 6, 1, 1, 2, 2, 2, 1] 33 rigid atoms, others: [32, 33, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087533 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=CC3=CC(C)=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 5, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 2, 2, 2, 10, 10, 21, 21, 21, 21, 21, 21] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087533 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087533/1 /scratch/stefan/7774412/working/building/REAL300004087533 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/670 `/scratch/stefan/7774412/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC3=CC(C)=CN=C32)S1) `REAL300004087533.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087533/1/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: REAL300004087533 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC3=CC(C)=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 5, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 201, 201, 201, 164, 72, 26, 6, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 201, 201, 6, 6, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [32, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087533 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=CC3=CC(C)=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 1, 1, 1, 5, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 41, 41, 92, 164, 164, 164, 164, 164, 164, 164, 164, 164, 1, 2, 2, 2, 3, 3, 92, 92, 164, 164, 164, 164, 164, 164] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087533 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087533 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087533/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087533/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087533 Building REAL300004087534 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087534' /scratch/stefan/7774412/working/building/REAL300004087534 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087534 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087534/0 /scratch/stefan/7774412/working/building/REAL300004087534 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/671 `/scratch/stefan/7774412/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCCO3)N=C2)S1) `REAL300004087534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087534 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCCO3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 19, 24, 24, 11, 7, 7, 1, 7, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 1, 1, 11, 11, 11, 11, 19, 19, 7, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [10, 43, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087534 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCCO3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 11, 11, 11, 62, 115, 115, 115, 115, 115, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 62, 62, 115, 115, 115, 115, 115, 115, 115, 115, 115, 11] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087534 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CCCCO3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 5, 12, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 201, 201, 201, 115, 80, 80, 21, 80, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 21, 21, 115, 115, 115, 115, 201, 201, 80, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 781 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087534 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087534 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087534/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087534 Building REAL300004087535 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087535' /scratch/stefan/7774412/working/building/REAL300004087535 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087535 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087535/0 /scratch/stefan/7774412/working/building/REAL300004087535 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/672 `/scratch/stefan/7774412/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=C2CCCCCC3)S1) `REAL300004087535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087535 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=C2CCCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 29, 29, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 29, 29, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 116 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087535 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=C2CCCCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 54 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087535 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087535 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087535/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087535 Building REAL300004087536 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087536' /scratch/stefan/7774412/working/building/REAL300004087536 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087536 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087536/0 /scratch/stefan/7774412/working/building/REAL300004087536 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/673 `/scratch/stefan/7774412/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC=CN3C=N2)S1) `REAL300004087536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087536 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC=CN3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 24, 25, 25, 16, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 24, 24, 11, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087536 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC=CN3C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087536 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087536 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087536/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087536 Building REAL300004087537 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087537' /scratch/stefan/7774412/working/building/REAL300004087537 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087537 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087537/0 /scratch/stefan/7774412/working/building/REAL300004087537 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/674 `/scratch/stefan/7774412/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC=C(C)C3=C2)S1) `REAL300004087537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087537 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC=C(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 19, 19, 19, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 9, 1, 1, 1, 2, 2, 2, 1] 19 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087537 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC=C(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087537 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087537 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087537/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087537 Building REAL300004087538 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087538' /scratch/stefan/7774412/working/building/REAL300004087538 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087538 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087538/0 /scratch/stefan/7774412/working/building/REAL300004087538 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/675 `/scratch/stefan/7774412/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=C2CCC(C)(C)C3)S1) `REAL300004087538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087538 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=C2CCC(C)(C)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 33, 33, 33, 18, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 33, 33, 11, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 33 rigid atoms, others: [32, 33, 34, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087538 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=C2CCC(C)(C)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087538 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087538 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087538/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087538 Building REAL300004087539 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087539' /scratch/stefan/7774412/working/building/REAL300004087539 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087539 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087539/0 /scratch/stefan/7774412/working/building/REAL300004087539 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/676 `/scratch/stefan/7774412/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC3=CC=NC=C32)S1) `REAL300004087539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087539 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC3=CC=NC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 1, 2, 2, 2, 1, 1, 1, 1] 13 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087539 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC3=CC=NC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087539 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087539 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087539/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087539 Building REAL300004087540 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087540' /scratch/stefan/7774412/working/building/REAL300004087540 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087540 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087540/0 /scratch/stefan/7774412/working/building/REAL300004087540 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/677 `/scratch/stefan/7774412/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCOCCOC(C)(C)C)S1) `REAL300004087540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087540 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCOCCOC(C)(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 2, 4, 12, 25, 38, 42, 42, 42, 42, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 25, 25, 38, 38, 42, 42, 42, 42, 42, 42, 42, 42, 42] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087540 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087540 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087540/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087540 Building REAL300004087541 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087541' /scratch/stefan/7774412/working/building/REAL300004087541 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087541 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087541/0 /scratch/stefan/7774412/working/building/REAL300004087541 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/678 `/scratch/stefan/7774412/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCC(C(C)C)C3)S2)S1) `REAL300004087541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087541 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCC(C(C)C)C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 20, 38, 42, 42, 19, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 1, 19, 20, 20, 20, 38, 38, 13, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1] 58 rigid atoms, others: [32, 33, 34, 35, 36, 44, 10, 45, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087541 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCC(C(C)C)C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 20, 31, 31, 20, 19, 1, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 31, 31, 31, 31, 31, 31, 31, 20, 20] 58 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087541 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087541 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087541/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087541 Building REAL300004087542 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087542' /scratch/stefan/7774412/working/building/REAL300004087542 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087542 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087542/0 /scratch/stefan/7774412/working/building/REAL300004087542 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/679 `/scratch/stefan/7774412/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3C=NN(C)C3=C2)S1) `REAL300004087542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087542 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3C=NN(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 2, 2, 2, 1] 25 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087542 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3C=NN(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087542 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087542 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087542/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087542 Building REAL300004087543 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087543' /scratch/stefan/7774412/working/building/REAL300004087543 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087543 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087543/0 /scratch/stefan/7774412/working/building/REAL300004087543 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/680 `/scratch/stefan/7774412/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087543 none CCOCCOCCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [141, 139, 103, 90, 38, 16, 10, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 141, 141, 141, 141, 141, 103, 103, 90, 90, 16, 16, 10, 10, 2, 2, 2, 2, 2, 2] 189 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 504 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087543 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087543 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087543/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087543 Building REAL300004087544 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087544' /scratch/stefan/7774412/working/building/REAL300004087544 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087544 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087544/0 /scratch/stefan/7774412/working/building/REAL300004087544 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/681 `/scratch/stefan/7774412/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(F)C=C2)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087544 none CC1=NN(C2=CC=C(F)C=C2)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 24, 24, 24, 35, 35, 35, 24, 24, 24, 4, 4, 4, 1, 1, 1, 1, 4, 19, 35, 35, 24, 24, 24] 35 rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 117 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087544 none CC1=NN(C2=CC=C(F)C=C2)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 1, 1, 12, 12, 12, 19, 19, 20, 35, 35, 35, 19, 19, 19, 2, 2, 2, 4, 4, 4, 4, 1, 12, 35, 35, 20, 20, 20] 35 rigid atoms, others: [0, 1, 2, 3, 4, 33, 11, 12, 13] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 152 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087544 none CC1=NN(C2=CC=C(F)C=C2)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 19, 19, 19, 24, 24, 20, 20, 24, 24, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 24, 24, 24, 24, 20, 2, 2, 2, 2, 2, 2] 35 rigid atoms, others: [15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087544 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087544 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087544/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087544 Building REAL300004087545 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087545' /scratch/stefan/7774412/working/building/REAL300004087545 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087545 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087545/0 /scratch/stefan/7774412/working/building/REAL300004087545 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/682 `/scratch/stefan/7774412/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2(C)CCOCC2)S1) `REAL300004087545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087545 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2(C)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 10, 10, 10, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087545 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2(C)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087545 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087545/1 /scratch/stefan/7774412/working/building/REAL300004087545 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/683 `/scratch/stefan/7774412/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2(C)CCOCC2)S1) `REAL300004087545.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087545/1/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: REAL300004087545 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2(C)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 96, 59, 15, 59, 6, 1, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 201, 201, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 537 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087545 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2(C)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 30, 30, 59, 109, 167, 167, 167, 167, 167, 167, 1, 2, 2, 2, 2, 2, 59, 59, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 542 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087545 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087545 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087545/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087545/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087545 Building REAL300004087546 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087546' /scratch/stefan/7774412/working/building/REAL300004087546 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087546 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087546/0 /scratch/stefan/7774412/working/building/REAL300004087546 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/684 `/scratch/stefan/7774412/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN=C3C(C)=CC=CN23)S1) `REAL300004087546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087546 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN=C3C(C)=CC=CN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 1, 1, 5, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 5, 5, 1, 2, 2, 2, 1, 1, 1] 15 rigid atoms, others: [32, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087546 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN=C3C(C)=CC=CN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 1, 1, 5, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 9] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087546 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087546 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087546/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087546 Building REAL300004087547 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087547' /scratch/stefan/7774412/working/building/REAL300004087547 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087547 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087547/0 /scratch/stefan/7774412/working/building/REAL300004087547 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/685 `/scratch/stefan/7774412/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2CCCO2)S1) `REAL300004087547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087547 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 14, 14, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 11, 11, 6, 1, 1, 5, 5, 5, 5, 5, 5, 5] 18 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087547 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 3, 6, 6, 11, 11, 11, 11, 11, 11, 11] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087547 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 18, 18, 18, 11, 11, 11, 5, 11, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087547 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087547 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087547/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087547 Building REAL300004087548 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087548' /scratch/stefan/7774412/working/building/REAL300004087548 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087548 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087548/0 /scratch/stefan/7774412/working/building/REAL300004087548 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/686 `/scratch/stefan/7774412/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(S(C)(=O)=O)C=C2)S1) `REAL300004087548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087548 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 37, 41, 41, 19, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 19, 19, 37, 37, 11, 4, 4, 1, 1, 3, 3, 3, 1, 1] 66 rigid atoms, others: [32, 33, 37, 38, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 185 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087548 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(S(C)(=O)=O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 12, 35, 35, 35, 19, 19, 1, 2, 2, 2, 3, 3, 2, 9, 9, 19, 19, 35, 35, 35, 19, 19] 66 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087548 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087548 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087548/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087548 Building REAL300004087549 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087549' /scratch/stefan/7774412/working/building/REAL300004087549 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087549 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087549/0 /scratch/stefan/7774412/working/building/REAL300004087549 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/687 `/scratch/stefan/7774412/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1) `REAL300004087549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087549 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 37, 40, 40, 19, 11, 11, 1, 11, 1, 1, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 37, 37, 11, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 102 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 169 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087549 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 58, 58, 58, 58, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 58, 58, 58, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 102 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087549 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 102, 102, 102, 58, 37, 37, 10, 37, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 58, 58, 58, 58, 102, 102, 37, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 102 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 391 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087549 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087549/1 /scratch/stefan/7774412/working/building/REAL300004087549 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/688 `/scratch/stefan/7774412/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1) `REAL300004087549.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087549 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 165, 167, 167, 130, 42, 8, 1, 8, 1, 1, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 165, 165, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087549 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 55, 55, 130, 170, 170, 170, 170, 130, 130, 130, 130, 130, 130, 1, 2, 2, 2, 2, 2, 170, 170, 170, 130, 130, 130, 130, 130, 130, 130, 130, 130, 130] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087549 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CS3)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 170, 201, 201, 201, 170, 90, 37, 10, 37, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 170, 170, 170, 170, 201, 201, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 466 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087549 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087549 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087549/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087549/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087549 Building REAL300004087550 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087550' /scratch/stefan/7774412/working/building/REAL300004087550 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087550 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087550/0 /scratch/stefan/7774412/working/building/REAL300004087550 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/689 `/scratch/stefan/7774412/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CC=C2)=CO1) `REAL300004087550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087550 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CC=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 22, 22, 38, 38, 32, 38, 38, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 38, 38, 32, 38, 38, 22] 62 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087550 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CC=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 13, 22, 22, 22, 42, 58, 58, 22, 22, 22, 1, 1, 6, 6, 2, 6, 6, 1, 1, 2, 2, 2, 13, 42, 42, 22, 22, 22, 6, 6, 2, 6, 6, 1] 62 rigid atoms, others: [0, 1, 2, 3, 39, 16, 17, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 253 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087550 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CC=CC=C2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 21, 21, 25, 38, 38, 38, 62, 62, 62, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 25, 62, 62, 38, 38, 38, 1, 1, 1, 1, 1, 6] 62 rigid atoms, others: [34, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39]) total number of confs: 231 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087550 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087550 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087550/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087550 Building REAL300004087551 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087551' /scratch/stefan/7774412/working/building/REAL300004087551 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087551 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087551/0 /scratch/stefan/7774412/working/building/REAL300004087551 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/690 `/scratch/stefan/7774412/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(F)(F)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N1) `REAL300004087551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087551 none CC1=C(CC(F)(F)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 15, 15, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 113, 92, 41, 92, 92, 9, 41, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 113, 113, 2, 2, 2, 2, 2, 165, 165, 165, 165, 165] 201 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 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: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087551 none CC1=C(CC(F)(F)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 15, 15, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 7, 37, 37, 95, 165, 165, 165, 201, 201, 201, 165, 165, 165, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 201, 201, 165, 165, 165, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 37, 38, 39, 40, 41, 20, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 512 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087551 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087551/1 /scratch/stefan/7774412/working/building/REAL300004087551 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/691 `/scratch/stefan/7774412/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(F)(F)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N1) `REAL300004087551.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087551/1/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: REAL300004087551 none CC1=C(CC(F)(F)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 15, 15, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [129, 129, 70, 18, 3, 18, 18, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 129, 129, 129, 70, 70, 2, 2, 2, 2, 2, 2, 129, 129, 129, 129, 129] 179 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 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: 408 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087551 none CC1=C(CC(F)(F)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 15, 15, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 19, 19, 19, 79, 79, 81, 129, 129, 129, 179, 179, 179, 129, 129, 129, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 81, 179, 179, 129, 129, 129, 1, 1, 1, 1, 1] 179 rigid atoms, others: [0, 1, 2, 3, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087551 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087551 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087551/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087551/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087551 Building REAL300004087552 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087552' /scratch/stefan/7774412/working/building/REAL300004087552 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087552 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087552/0 /scratch/stefan/7774412/working/building/REAL300004087552 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/692 `/scratch/stefan/7774412/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(Cl)C=CC=C2OCC2CC2)S1) `REAL300004087552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087552 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(Cl)C=CC=C2OCC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 5, 13, 13, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 45, 45, 3, 3, 3, 3, 5, 5, 3, 1, 1, 1, 29, 29, 45, 45, 45, 45, 45] 69 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 183 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087552 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(Cl)C=CC=C2OCC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 15, 40, 54, 54, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 40, 40, 54, 54, 54, 54, 54] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087552 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(Cl)C=CC=C2OCC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 16, 1, 1, 1, 1, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 69, 69, 69, 54, 54, 54, 45, 54, 45, 45, 45, 45, 45, 45, 30, 10, 1, 1, 1, 1, 54, 54, 54, 54, 69, 69, 54, 45, 45, 45, 10, 10, 1, 1, 1, 1, 1] 69 rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 209 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087552 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087552 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087552/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087552 Building REAL300004087553 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087553' /scratch/stefan/7774412/working/building/REAL300004087553 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087553 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087553/0 /scratch/stefan/7774412/working/building/REAL300004087553 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/693 `/scratch/stefan/7774412/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCCC2)=NO1) `REAL300004087553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087553 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCCC2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 25, 25, 86, 86, 86, 86, 86, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86] 151 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 230 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087553 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCCC2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 14, 25, 25, 25, 49, 67, 67, 25, 25, 25, 1, 1, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2, 14, 49, 49, 25, 25, 25, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 151 rigid atoms, others: [0, 1, 2, 3, 16, 17, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087553 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCCC2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 10, 44, 44, 56, 86, 86, 86, 151, 151, 151, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 11, 11, 56, 151, 151, 86, 86, 86, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 151 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 599 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087553 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087553 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087553/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087553 Building REAL300004087554 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087554' /scratch/stefan/7774412/working/building/REAL300004087554 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087554 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087554/0 /scratch/stefan/7774412/working/building/REAL300004087554 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/694 `/scratch/stefan/7774412/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCC2)=NO1) `REAL300004087554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087554 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCC2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 24, 24, 81, 81, 81, 81, 24, 24, 24, 24, 24, 2, 2, 2, 2, 2, 2, 81, 81, 81, 81, 81, 81, 81, 81, 81] 140 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 219 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087554 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCC2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 14, 24, 24, 24, 47, 78, 78, 24, 24, 24, 1, 1, 8, 8, 8, 8, 1, 1, 2, 2, 2, 14, 47, 47, 24, 24, 24, 8, 8, 8, 8, 8, 8, 8, 8, 8] 140 rigid atoms, others: [0, 1, 2, 3, 16, 17, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 333 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087554 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2CCCC2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 42, 42, 51, 81, 81, 81, 140, 140, 140, 81, 81, 81, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 51, 140, 140, 81, 81, 81, 1, 1, 1, 1, 1, 1, 1, 1, 1] 140 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 539 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087554 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087554 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087554/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087554 Building REAL300004087555 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087555' /scratch/stefan/7774412/working/building/REAL300004087555 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087555 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087555/0 /scratch/stefan/7774412/working/building/REAL300004087555 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/695 `/scratch/stefan/7774412/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087555 none CC1=CSC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 11, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 21, 21, 21, 21, 21, 11, 11, 2, 2, 2, 2, 2, 2, 21] 27 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087555 none CC1=CSC(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 21, 21, 21, 21, 21, 21, 27, 27, 27, 21, 21, 21, 1, 2, 2, 2, 1, 7, 7, 21, 27, 27, 21, 21, 21, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087555 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087555 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087555/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087555 Building REAL300004087556 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087556' /scratch/stefan/7774412/working/building/REAL300004087556 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087556 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087556/0 /scratch/stefan/7774412/working/building/REAL300004087556 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/696 `/scratch/stefan/7774412/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC=C2OCC(C)C)S1) `REAL300004087556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087556 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC=C2OCC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 41, 41, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19, 24, 29, 13, 13, 13, 13, 25, 25, 8, 1, 1, 1, 19, 19, 29, 29, 29, 29, 29, 29, 29] 108 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087556 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Cl)=CC=C2OCC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 3, 13, 13, 13, 41, 67, 75, 78, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 67, 67, 78, 78, 78, 78, 78, 78, 78] 108 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087556 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087556 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087556/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087556 Building REAL300004087557 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087557' /scratch/stefan/7774412/working/building/REAL300004087557 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087557 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087557/0 /scratch/stefan/7774412/working/building/REAL300004087557 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/697 `/scratch/stefan/7774412/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CN(C)N=C3)CCCO2)S1) `REAL300004087557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087557 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CN(C)N=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 31, 58, 58, 16, 11, 11, 1, 11, 1, 1, 11, 11, 11, 11, 11, 1, 1, 1, 1, 16, 16, 16, 16, 31, 31, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [35, 36, 37, 38, 39, 40, 10, 12, 13, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 234 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087557 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CN(C)N=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 16, 55, 55, 55, 55, 55, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 2, 55, 55, 55, 55, 55, 16, 16, 16, 16, 16, 16] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 118 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087557 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CN(C)N=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 82, 82, 82, 55, 40, 40, 11, 40, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 55, 55, 55, 55, 82, 82, 40, 1, 2, 2, 2, 1, 11, 11, 11, 11, 11, 11] 82 rigid atoms, others: [34, 12, 13, 14, 15, 16, 17, 18, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 297 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087557 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087557/1 /scratch/stefan/7774412/working/building/REAL300004087557 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/698 `/scratch/stefan/7774412/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CN(C)N=C3)CCCO2)S1) `REAL300004087557.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087557 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CN(C)N=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 146, 158, 158, 125, 44, 12, 1, 12, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 125, 125, 125, 125, 146, 146, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087557 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CN(C)N=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 43, 43, 125, 182, 182, 182, 182, 182, 125, 125, 125, 125, 1, 2, 2, 2, 2, 2, 182, 182, 182, 182, 182, 125, 125, 125, 125, 125, 125] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 448 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087557 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CN(C)N=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 8, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 201, 201, 201, 182, 84, 39, 10, 39, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 182, 182, 182, 182, 201, 201, 1, 2, 2, 2, 1, 10, 10, 10, 10, 10, 10] 201 rigid atoms, others: [33, 12, 13, 14, 15, 16, 17, 18, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 423 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087557 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087557 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087557/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087557/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087557 Building REAL300004087558 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087558' /scratch/stefan/7774412/working/building/REAL300004087558 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087558 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087558/0 /scratch/stefan/7774412/working/building/REAL300004087558 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/699 `/scratch/stefan/7774412/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC1=CC=CC(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087558 none COCCOC1=CC=CC(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [108, 85, 41, 40, 15, 15, 15, 15, 15, 6, 6, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 108, 108, 108, 85, 85, 41, 41, 15, 15, 15, 6, 6, 2, 2, 2, 2, 2, 2, 15] 120 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 348 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087558 none COCCOC1=CC=CC(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [43, 16, 7, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 15, 27, 46, 46, 15, 15, 15, 1, 43, 43, 43, 16, 16, 7, 7, 1, 1, 1, 5, 5, 15, 27, 27, 15, 15, 15, 1] 120 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 44, 25] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 268 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087558 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087558 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087558/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087558 Building REAL300004087559 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087559' /scratch/stefan/7774412/working/building/REAL300004087559 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087559 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087559/0 /scratch/stefan/7774412/working/building/REAL300004087559 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/700 `/scratch/stefan/7774412/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2N2C=CC=N2)S1) `REAL300004087559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087559 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2N2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 31, 53, 53, 53, 31, 23, 23, 7, 23, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 31, 31, 31, 31, 53, 53, 23, 7, 7, 1, 1, 1, 1, 4, 4, 4] 53 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087559 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2N2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 15, 15, 31, 31, 21, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 2, 2, 2, 15, 15, 31, 31, 31, 31, 31, 31, 31] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087559 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=CC=C2N2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [31, 31, 31, 31, 53, 53, 53, 31, 25, 25, 13, 25, 13, 4, 4, 4, 3, 4, 4, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 53, 53, 25, 13, 13, 4, 4, 4, 4, 1, 1, 1] 53 rigid atoms, others: [38, 39, 40, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 214 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087559 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087559 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087559/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087559 Building REAL300004087560 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087560' /scratch/stefan/7774412/working/building/REAL300004087560 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087560 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087560/0 /scratch/stefan/7774412/working/building/REAL300004087560 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/701 `/scratch/stefan/7774412/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C(F)(F)F)C=C2C)S1) `REAL300004087560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087560 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C(F)(F)F)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 42, 42, 42, 27, 27, 23, 8, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 42, 42, 24, 8, 8, 1, 1, 1, 2, 2, 2] 42 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) total number of confs: 168 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: REAL300004087560 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C(F)(F)F)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 13, 13, 27, 27, 13, 13, 27, 27, 27, 27, 27, 27, 1, 2, 2, 2, 2, 2, 2, 13, 13, 27, 27, 27, 27, 27, 27] 42 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087560 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087560 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087560/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087560 Building REAL300004087561 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087561' /scratch/stefan/7774412/working/building/REAL300004087561 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087561 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087561/0 /scratch/stefan/7774412/working/building/REAL300004087561 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/702 `/scratch/stefan/7774412/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C(F)(F)F)C(C)=C2)S1) `REAL300004087561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087561 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C(F)(F)F)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 32, 32, 32, 22, 22, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 32, 32, 22, 5, 5, 1, 1, 2, 2, 2, 1] 32 rigid atoms, others: [34, 35, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087561 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C(F)(F)F)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 10, 10, 22, 22, 10, 10, 22, 22, 22, 22, 22, 22, 1, 2, 2, 2, 3, 3, 2, 10, 10, 22, 22, 22, 22, 22, 22] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087561 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087561 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087561/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087561 Building REAL300004087562 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087562' /scratch/stefan/7774412/working/building/REAL300004087562 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087562 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087562/0 /scratch/stefan/7774412/working/building/REAL300004087562 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/703 `/scratch/stefan/7774412/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C3CC3)C=C2)S1) `REAL300004087562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087562 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 21, 25, 25, 17, 17, 17, 3, 17, 3, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 17, 17, 17, 17, 21, 21, 17, 3, 3, 1, 1, 7, 7, 7, 7, 7, 1, 1] 38 rigid atoms, others: [32, 33, 39, 40, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087562 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 11, 17, 17, 11, 11, 36, 36, 17, 17, 1, 2, 2, 2, 2, 2, 2, 11, 11, 17, 17, 36, 36, 36, 36, 36, 17, 17] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087562 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 38, 38, 38, 36, 36, 35, 10, 36, 10, 1, 1, 7, 7, 1, 1, 1, 1, 7, 7, 36, 36, 36, 36, 38, 38, 36, 10, 10, 7, 7, 1, 1, 1, 1, 1, 7, 7] 38 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 115 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087562 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087562 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087562/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087562 Building REAL300004087563 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087563' /scratch/stefan/7774412/working/building/REAL300004087563 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087563 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087563/0 /scratch/stefan/7774412/working/building/REAL300004087563 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/704 `/scratch/stefan/7774412/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C) `REAL300004087563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087563 none CCOC1=CC=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [67, 55, 7, 7, 29, 29, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 29, 29, 29, 67, 67, 67, 67, 67, 29, 29, 7, 7, 2, 3, 3, 2, 2, 2, 29, 29, 29, 29] 76 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 236 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: REAL300004087563 none CCOC1=CC=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [24, 7, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 29, 29, 29, 41, 63, 63, 29, 29, 29, 1, 1, 1, 24, 24, 24, 24, 24, 1, 1, 5, 5, 29, 41, 41, 29, 29, 29, 1, 2, 2, 2] 76 rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 22, 23, 24, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 305 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087563 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087563 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087563/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087563 Building REAL300004087564 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087564' /scratch/stefan/7774412/working/building/REAL300004087564 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087564 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087564/0 /scratch/stefan/7774412/working/building/REAL300004087564 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/705 `/scratch/stefan/7774412/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(OC(C)C)C(C)=C2)S1) `REAL300004087564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087564 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(OC(C)C)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 56, 80, 80, 36, 36, 36, 5, 36, 5, 1, 1, 1, 1, 1, 1, 8, 15, 15, 1, 1, 1, 36, 36, 36, 36, 56, 56, 36, 5, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 1] 115 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 46, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 339 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087564 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(OC(C)C)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 36, 36, 9, 9, 79, 91, 91, 36, 36, 36, 1, 2, 2, 2, 2, 2, 2, 9, 9, 36, 36, 91, 91, 91, 91, 91, 91, 91, 36, 36, 36, 36] 115 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 281 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087564 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087564 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087564/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087564 Building REAL300004087565 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087565' /scratch/stefan/7774412/working/building/REAL300004087565 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087565 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087565/0 /scratch/stefan/7774412/working/building/REAL300004087565 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/706 `/scratch/stefan/7774412/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3COCCN3C(C3=CC=CC=C3)=N2)S1) `REAL300004087565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087565 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3COCCN3C(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 11, 19, 32, 32, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 10, 11, 11, 11, 19, 18, 7, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5] 34 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087565 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3COCCN3C(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 23, 23, 13, 23, 23, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 23, 23, 14, 23, 23] 34 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087565 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3COCCN3C(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 12, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 34, 34, 34, 23, 18, 18, 5, 18, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 34, 34, 18, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1] 34 rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 116 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087565 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087565 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087565/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087565 Building REAL300004087566 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087566' /scratch/stefan/7774412/working/building/REAL300004087566 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087566 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087566/0 /scratch/stefan/7774412/working/building/REAL300004087566 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/707 `/scratch/stefan/7774412/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087566 none C=CCCCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 100, 51, 29, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 129, 129, 129, 96, 100, 55, 55, 29, 29, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 201 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 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: 584 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087566 none C=CCCCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 17, 7, 4, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 44, 44, 13, 13, 13, 1, 1, 39, 39, 39, 16, 17, 8, 8, 4, 4, 1, 1, 9, 25, 25, 13, 13, 13, 1, 1] 201 rigid atoms, others: [33, 34, 4, 5, 6, 7, 8, 9, 42, 41, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087566 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087566 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087566/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087566 Building REAL300004087567 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087567' /scratch/stefan/7774412/working/building/REAL300004087567 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087567 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087567/0 /scratch/stefan/7774412/working/building/REAL300004087567 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/708 `/scratch/stefan/7774412/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=CC3=NSN=C32)S1) `REAL300004087567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087567 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=CC3=NSN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 14, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 21, 21, 21, 15, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 21, 21, 15, 5, 5, 1, 1, 1] 21 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087567 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=CC3=NSN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'N.2', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 8, 14, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 10, 10, 15, 15, 15] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087567 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087567 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087567/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087567 Building REAL300004087568 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087568' /scratch/stefan/7774412/working/building/REAL300004087568 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087568 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087568/0 /scratch/stefan/7774412/working/building/REAL300004087568 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/709 `/scratch/stefan/7774412/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2CCCC3(CC3)S2(=O)=O)S1) `REAL300004087568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087568 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2CCCC3(CC3)S2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 20, 20, 20, 15, 14, 14, 7, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 20, 20, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087568 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2CCCC3(CC3)S2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 4, 4, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 3, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087568 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087568/1 /scratch/stefan/7774412/working/building/REAL300004087568 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/710 `/scratch/stefan/7774412/working/3D/710' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2CCCC3(CC3)S2(=O)=O)S1) `REAL300004087568.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087568/1/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: REAL300004087568 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2CCCC3(CC3)S2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 201, 201, 201, 184, 93, 33, 9, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 201, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 409 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087568 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2CCCC3(CC3)S2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 5, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 57, 57, 138, 184, 184, 184, 184, 184, 184, 184, 184, 184, 1, 2, 2, 2, 2, 2, 138, 138, 184, 184, 184, 184, 184, 184, 184, 184, 184, 184] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087568 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087568 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087568/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087568/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087568 Building REAL300004087569 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087569' /scratch/stefan/7774412/working/building/REAL300004087569 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087569 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087569/0 /scratch/stefan/7774412/working/building/REAL300004087569 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/711 `/scratch/stefan/7774412/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCS(N)(=O)=O)S1) `REAL300004087569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087569 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCS(N)(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 14, 8, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 10, 14, 26, 26, 26, 1, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 14, 14, 26, 26] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 141 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087569 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087569 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087569/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087569 Building REAL300004087570 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087570' /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087570 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087570/0 /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/712 `/scratch/stefan/7774412/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+]1CCCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1) `REAL300004087570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@@H+]1CCCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2] 3 rigid atoms, others: [38, 39, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 23 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@@H+]1CCCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 43, 44, 34, 35, 22, 36, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42]) total number of confs: 18 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087570/1 /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/713 `/scratch/stefan/7774412/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+]1CCCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1) `REAL300004087570.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087570/1/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: REAL300004087570 none CCC[N@H+]1CCCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 27 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@H+]1CCCC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 43, 44, 34, 35, 22, 36, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42]) total number of confs: 18 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087570/2 /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/714 `/scratch/stefan/7774412/working/3D/714' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+]1CCCC(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C1) `REAL300004087570.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087570/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@@H+]1CCCC(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 8, 8, 8, 8, 8, 8, 8, 5, 8, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 8, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 8, 8, 8, 3, 3, 2, 2, 2, 8, 8] 11 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@@H+]1CCCC(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 8, 8, 8, 8, 10, 10, 8, 8, 8, 1, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1] 11 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 34, 35, 22, 36, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41]) total number of confs: 43 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087570/3 /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/715 `/scratch/stefan/7774412/working/3D/715' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+]1CCCC(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C1) `REAL300004087570.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087570/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@H+]1CCCC(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 5, 5] 7 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 34 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087570 none CCC[N@H+]1CCCC(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1] 7 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 42, 43, 34, 35, 22, 36, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41]) total number of confs: 24 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087570 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087570 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087570/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087570/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087570/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087570/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087570 Building REAL300004087571 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087571' /scratch/stefan/7774412/working/building/REAL300004087571 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087571 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087571/0 /scratch/stefan/7774412/working/building/REAL300004087571 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/716 `/scratch/stefan/7774412/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2)S1) `REAL300004087571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087571 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 22, 22, 12, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 12, 12, 22, 22, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6] 34 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 99 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087571 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 11, 12, 12, 12, 18, 18, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 18, 18, 18, 18, 18] 34 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087571 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 34, 34, 34, 18, 15, 15, 6, 15, 6, 6, 5, 6, 6, 1, 1, 1, 1, 18, 18, 18, 18, 34, 34, 15, 6, 6, 6, 6, 1, 1, 1, 1, 1] 34 rigid atoms, others: [32, 33, 34, 35, 36, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 138 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087571 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087571 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087571/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087571 Building REAL300004087572 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087572' /scratch/stefan/7774412/working/building/REAL300004087572 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087572 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087572/0 /scratch/stefan/7774412/working/building/REAL300004087572 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/717 `/scratch/stefan/7774412/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N=C1) `REAL300004087572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087572 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 21, 21, 21, 21, 21, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10] 37 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087572 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=CC=CC=C2N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 6, 6, 8, 10, 10, 10, 20, 27, 27, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 20, 20, 11, 11, 11, 1, 1, 1, 1, 1] 37 rigid atoms, others: [1, 2, 3, 4, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23, 24, 36] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087572 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087572 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087572/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087572 Building REAL300004087573 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087573' /scratch/stefan/7774412/working/building/REAL300004087573 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087573 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087573/0 /scratch/stefan/7774412/working/building/REAL300004087573 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/718 `/scratch/stefan/7774412/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=C(C)N=C3S2)S1) `REAL300004087573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087573 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=C(C)N=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 8, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 14, 27, 27, 27, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 27, 27, 10, 1, 2, 2, 2, 1, 2, 2, 2] 27 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087573 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=C(C)N=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 5, 8, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 14, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 14, 14, 14, 13, 14, 14, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087573 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087573 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087573/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087573 Building REAL300004087574 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087574' /scratch/stefan/7774412/working/building/REAL300004087574 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087574 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087574/0 /scratch/stefan/7774412/working/building/REAL300004087574 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/719 `/scratch/stefan/7774412/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCO2)S1) `REAL300004087574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087574 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 30, 42, 42, 16, 10, 10, 1, 10, 1, 1, 7, 7, 7, 7, 1, 1, 1, 1, 16, 16, 16, 16, 30, 30, 10, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 56 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 179 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087574 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 31, 31, 31, 31, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 16, 16] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 113 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087574 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 56, 56, 56, 31, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 31, 31, 31, 31, 56, 56, 21, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 56 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41]) total number of confs: 219 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087574 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087574/1 /scratch/stefan/7774412/working/building/REAL300004087574 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/720 `/scratch/stefan/7774412/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCO2)S1) `REAL300004087574.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087574 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 14, 14, 14, 13, 8, 6, 1, 6, 1, 1, 2, 2, 2, 2, 1, 1, 1, 1, 13, 13, 13, 13, 14, 14, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [35, 36, 37, 38, 39, 40, 10, 12, 13, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087574 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 9, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087574 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 14, 14, 14, 13, 8, 6, 2, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 13, 13, 13, 13, 14, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 14 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40]) total number of confs: 33 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087574 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087574 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087574/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087574/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087574 Building REAL300004087575 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087575' /scratch/stefan/7774412/working/building/REAL300004087575 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087575 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087575/0 /scratch/stefan/7774412/working/building/REAL300004087575 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/721 `/scratch/stefan/7774412/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC=CS2)S1) `REAL300004087575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087575 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 41, 41, 41, 29, 28, 26, 10, 26, 10, 1, 1, 1, 1, 1, 1, 29, 30, 30, 30, 41, 41, 28, 10, 10, 1, 1] 41 rigid atoms, others: [13, 14, 15, 16, 17, 18, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087575 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 29, 29, 29, 29, 1, 2, 2, 2, 3, 3, 2, 16, 16, 29, 29] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087575 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087575 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087575/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087575 Building REAL300004087576 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087576' /scratch/stefan/7774412/working/building/REAL300004087576 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087576 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087576/0 /scratch/stefan/7774412/working/building/REAL300004087576 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/722 `/scratch/stefan/7774412/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(F)C=C2F)S1) `REAL300004087576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087576 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(F)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 29, 29, 29, 23, 23, 23, 11, 23, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 29, 29, 23, 11, 11, 1, 1, 1] 29 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 99 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087576 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=C(F)C=C2F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 23, 23, 18, 23, 23, 23, 23, 1, 2, 2, 2, 2, 2, 2, 9, 9, 23, 23, 23] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087576 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087576 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087576/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087576 Building REAL300004087577 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087577' /scratch/stefan/7774412/working/building/REAL300004087577 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087577 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087577/0 /scratch/stefan/7774412/working/building/REAL300004087577 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/723 `/scratch/stefan/7774412/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C) `REAL300004087577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087577 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 6, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 17, 17, 17, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 33 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087577 none COC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 29, 29, 13, 13, 13, 1, 1, 1, 4, 4, 4, 1, 1, 9, 25, 25, 13, 13, 13, 1, 2, 2, 2] 33 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087577 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087577 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087577/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087577 Building REAL300004087578 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087578' /scratch/stefan/7774412/working/building/REAL300004087578 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087578 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087578/0 /scratch/stefan/7774412/working/building/REAL300004087578 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/724 `/scratch/stefan/7774412/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=CS1) `REAL300004087578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087578 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 32, 32, 32, 2, 2, 2, 2, 2, 2, 20, 20] 36 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 75 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087578 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 1, 1, 12, 12, 15, 20, 20, 20, 32, 36, 36, 20, 20, 20, 1, 1, 1, 9, 9, 9, 15, 32, 32, 20, 20, 20, 1, 1] 36 rigid atoms, others: [1, 2, 3, 4, 17, 18, 19, 29, 30] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087578 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087578 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087578/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087578 Building REAL300004087579 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087579' /scratch/stefan/7774412/working/building/REAL300004087579 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087579 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087579/0 /scratch/stefan/7774412/working/building/REAL300004087579 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/725 `/scratch/stefan/7774412/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(S(=O)(=O)N(C)C)CC2)S1) `REAL300004087579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087579 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(S(=O)(=O)N(C)C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 35, 53, 53, 17, 14, 12, 1, 12, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 1, 1, 17, 18, 18, 18, 35, 35, 14, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 75 rigid atoms, others: [32, 33, 34, 35, 44, 10, 43, 12, 13, 14, 15, 16, 22, 23, 45, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087579 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCN(S(=O)(=O)N(C)C)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 14, 11, 11, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 51, 51, 51, 55, 55, 17, 17, 1, 2, 2, 2, 3, 3, 2, 17, 17, 17, 17, 17, 55, 55, 55, 55, 55, 55, 17, 17, 17, 17] 75 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087579 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087579 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087579/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087579 Building REAL300004087580 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087580' /scratch/stefan/7774412/working/building/REAL300004087580 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087580 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087580/0 /scratch/stefan/7774412/working/building/REAL300004087580 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/726 `/scratch/stefan/7774412/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CN=CC(Br)=C2)S1) `REAL300004087580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087580 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CN=CC(Br)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 35, 35, 35, 19, 19, 17, 13, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 35, 35, 19, 13, 13, 7, 7, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087580 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CN=CC(Br)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 8, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 6, 8, 19, 19, 18, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 6, 6, 8, 8, 19, 19, 19] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087580 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087580 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087580/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087580 Building REAL300004087581 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087581' /scratch/stefan/7774412/working/building/REAL300004087581 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087581 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087581/0 /scratch/stefan/7774412/working/building/REAL300004087581 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/727 `/scratch/stefan/7774412/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(F)=CC(OC(F)F)=C2)S1) `REAL300004087581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087581 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(F)=CC(OC(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 9, 1] 9 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087581 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(F)=CC(OC(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 15, 1, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 5, 9, 9, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 9, 3] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087581 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087581 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087581/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087581 Building REAL300004087582 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087582' /scratch/stefan/7774412/working/building/REAL300004087582 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087582 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087582/0 /scratch/stefan/7774412/working/building/REAL300004087582 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/728 `/scratch/stefan/7774412/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087582 none CCCCCCCCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 79, 63, 47, 31, 15, 11, 11, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 11, 11, 95, 95, 95, 95, 95, 95, 95, 79, 79, 63, 63, 47, 47, 31, 31, 15, 15, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11] 185 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 428 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087582 none CCCCCCCCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 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, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 11, 9, 7, 5, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 31, 31, 11, 11, 11, 1, 1, 13, 13, 13, 13, 13, 13, 13, 11, 11, 9, 9, 7, 7, 5, 5, 3, 3, 1, 1, 7, 21, 21, 11, 11, 11, 1, 1] 185 rigid atoms, others: [7, 8, 9, 10, 11, 44, 45, 12, 52, 53, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087582 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087582 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087582/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087582 Building REAL300004087583 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087583' /scratch/stefan/7774412/working/building/REAL300004087583 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087583 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087583/0 /scratch/stefan/7774412/working/building/REAL300004087583 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/729 `/scratch/stefan/7774412/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CN=C2)CC3)S1) `REAL300004087583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087583 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CN=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 16, 16, 8, 7, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 15, 15, 7, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 39, 40, 41, 10, 12, 13, 14, 15, 16, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087583 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CN=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 16, 16, 16, 16, 8, 8, 8, 8] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087583 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CN=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 24, 24, 24, 16, 15, 13, 5, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 24, 24, 15, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5] 24 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 86 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087583 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087583 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087583/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087583 Building REAL300004087584 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087584' /scratch/stefan/7774412/working/building/REAL300004087584 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087584 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087584/0 /scratch/stefan/7774412/working/building/REAL300004087584 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/730 `/scratch/stefan/7774412/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCC1) `REAL300004087584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087584 none COCC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [78, 68, 47, 18, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 47, 47, 47, 47, 78, 78, 78, 68, 68, 18, 18, 2, 2, 2, 2, 2, 2, 47, 47, 47, 47, 47, 47, 47, 47] 112 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 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: 310 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087584 none COCC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [19, 10, 1, 1, 1, 10, 35, 35, 39, 47, 47, 47, 80, 94, 94, 47, 47, 47, 1, 1, 1, 1, 19, 19, 19, 10, 10, 10, 10, 39, 80, 80, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1] 112 rigid atoms, others: [35, 2, 3, 4, 37, 38, 39, 40, 41, 42, 18, 19, 20, 21, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 423 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087584 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087584 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087584/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087584 Building REAL300004087585 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087585' /scratch/stefan/7774412/working/building/REAL300004087585 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087585 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087585/0 /scratch/stefan/7774412/working/building/REAL300004087585 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/731 `/scratch/stefan/7774412/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CC=C3)CCCCO2)S1) `REAL300004087585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087585 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CC=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 16, 16, 7, 5, 5, 1, 5, 1, 1, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 5, 6, 6, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 76 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: REAL300004087585 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CC=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 7, 12, 12, 8, 12, 12, 7, 7, 7, 7, 7, 1, 2, 2, 2, 3, 3, 2, 12, 12, 9, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087585 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC=CC=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 18, 18, 18, 12, 9, 9, 6, 9, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 12, 12, 12, 12, 18, 18, 9, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 18 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087585 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087585/1 /scratch/stefan/7774412/working/building/REAL300004087585 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/732 `/scratch/stefan/7774412/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CC=C3)CCCCO2)S1) `REAL300004087585.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087585 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CC=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 169, 185, 185, 114, 25, 6, 1, 6, 1, 1, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 114, 114, 114, 114, 169, 169, 7, 7, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 555 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087585 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CC=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 61, 61, 110, 167, 167, 138, 167, 167, 114, 114, 114, 114, 114, 1, 2, 2, 2, 2, 2, 167, 167, 143, 167, 167, 114, 114, 114, 114, 114, 114, 114, 114] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 525 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087585 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC=CC=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 64, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 167, 167, 167, 167, 201, 201, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 454 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087585 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087585 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087585/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087585/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087585 Building REAL300004087586 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087586' /scratch/stefan/7774412/working/building/REAL300004087586 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087586 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087586/0 /scratch/stefan/7774412/working/building/REAL300004087586 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/733 `/scratch/stefan/7774412/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C2=CC=CC=C2F)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087586 none CC1=CN(C2=CC=CC=C2F)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 30, 30, 30, 47, 48, 48, 30, 30, 30, 9, 9, 9, 8, 1, 1, 1, 1, 24, 48, 47, 31, 31, 31] 48 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087586 none CC1=CN(C2=CC=CC=C2F)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 1, 8, 8, 8, 1, 1, 1, 9, 9, 9, 12, 12, 12, 24, 31, 31, 12, 12, 12, 2, 2, 2, 1, 8, 8, 2, 8, 9, 25, 24, 13, 13, 13] 48 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 29] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087586 none CC1=CN(C2=CC=CC=C2F)N=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 15, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 30, 30, 17, 30, 30, 30, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 13, 12, 30, 30, 25, 30, 2, 2, 2, 2, 2, 2] 48 rigid atoms, others: [15, 16, 17, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087586 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087586 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087586/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087586 Building REAL300004087587 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087587' /scratch/stefan/7774412/working/building/REAL300004087587 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087587 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087587/0 /scratch/stefan/7774412/working/building/REAL300004087587 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/734 `/scratch/stefan/7774412/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCOCC3)=NN2C)S1) `REAL300004087587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087587 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCOCC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 31, 39, 39, 17, 12, 12, 1, 12, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 1, 17, 17, 17, 17, 31, 31, 12, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 131 rigid atoms, others: [10, 12, 13, 14, 15, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087587 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCOCC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 17, 17, 17, 75, 75, 75, 75, 75, 17, 17, 17, 1, 2, 2, 2, 2, 2, 2, 17, 75, 75, 75, 75, 75, 75, 75, 75, 75, 17, 17, 17] 131 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 199 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087587 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCOCC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 12, 5, 5, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 131, 131, 131, 75, 57, 57, 13, 57, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 75, 75, 75, 75, 131, 131, 57, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 131 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43]) total number of confs: 492 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087587 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087587 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087587/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087587 Building REAL300004087588 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087588' /scratch/stefan/7774412/working/building/REAL300004087588 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087588 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087588/0 /scratch/stefan/7774412/working/building/REAL300004087588 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/735 `/scratch/stefan/7774412/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1=CC=CC=C1F) `REAL300004087588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087588 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 11, 37, 37, 11, 37, 37, 37, 12, 12, 12, 11, 2, 2, 2, 2, 2, 2, 37, 37, 36, 37] 63 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087588 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 11, 11, 11, 18, 19, 19, 11, 11, 11, 1, 1, 1, 5, 5, 1, 5, 5, 5, 2, 2, 2, 1, 10, 18, 18, 12, 12, 12, 5, 5, 4, 5] 63 rigid atoms, others: [0, 1, 2, 3, 4, 17, 18, 19, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087588 none CC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C1=CC=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 1, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 33, 33, 33, 37, 37, 37, 63, 63, 63, 37, 37, 37, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 33, 63, 63, 37, 37, 37, 1, 1, 1, 1] 63 rigid atoms, others: [36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087588 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087588 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087588/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087588 Building REAL300004087589 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087589' /scratch/stefan/7774412/working/building/REAL300004087589 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087589 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087589/0 /scratch/stefan/7774412/working/building/REAL300004087589 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/736 `/scratch/stefan/7774412/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)SC(S(N)(=O)=O)=C2)S1) `REAL300004087589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087589 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)SC(S(N)(=O)=O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 14, 1, 14, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 27, 27, 27, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 14, 14, 14, 14, 27, 27, 10, 1, 1, 1, 5, 5, 1] 91 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087589 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)SC(S(N)(=O)=O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.o2', 'N.pl3', 'O.2', 'O.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 14, 1, 14, 8, 11, 11, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 49, 49, 49, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 49, 49, 14] 91 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087589 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087589 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087589/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087589 Building REAL300004087590 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087590' /scratch/stefan/7774412/working/building/REAL300004087590 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087590 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087590/0 /scratch/stefan/7774412/working/building/REAL300004087590 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/737 `/scratch/stefan/7774412/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C(OC(F)F)=C2)S1) `REAL300004087590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087590 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C(OC(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 2, 2, 5, 1] 5 rigid atoms, others: [36, 10, 12, 13, 14, 15, 16, 17, 18, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 28 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087590 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C)C(OC(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 12, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 5, 5, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 5, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087590 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087590 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087590/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087590 Building REAL300004087591 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087591' /scratch/stefan/7774412/working/building/REAL300004087591 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087591 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087591/0 /scratch/stefan/7774412/working/building/REAL300004087591 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/738 `/scratch/stefan/7774412/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC2=CC=CC=C21) `REAL300004087591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087591 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 24, 24, 24, 24, 24, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 42 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087591 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)SC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 23, 24, 24, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 2, 2, 9, 23, 23, 13, 13, 13, 1, 1, 1, 1] 42 rigid atoms, others: [1, 2, 3, 4, 37, 35, 17, 18, 19, 20, 21, 22, 23, 36, 38] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087591 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087591 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087591/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087591 Building REAL300004087592 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087592' /scratch/stefan/7774412/working/building/REAL300004087592 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087592 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087592/0 /scratch/stefan/7774412/working/building/REAL300004087592 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/739 `/scratch/stefan/7774412/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)CC2CCCCC2)S1) `REAL300004087592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087592 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)CC2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 85, 85, 85, 49, 32, 32, 9, 32, 5, 9, 9, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 85, 85, 32, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 347 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087592 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)CC2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 20, 20, 20, 43, 49, 49, 49, 49, 49, 1, 2, 2, 2, 2, 2, 2, 21, 21, 21, 43, 43, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 85 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087592 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087592 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087592/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087592 Building REAL300004087593 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087593' /scratch/stefan/7774412/working/building/REAL300004087593 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087593 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087593/0 /scratch/stefan/7774412/working/building/REAL300004087593 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/740 `/scratch/stefan/7774412/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C3C(=C2)C=NN3C)S1) `REAL300004087593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087593 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C3C(=C2)C=NN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 73, 73, 73, 37, 21, 21, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 73, 73, 21, 7, 7, 1, 1, 1, 1, 2, 2, 2] 73 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087593 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C3C(=C2)C=NN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 3, 3, 2, 9, 9, 37, 37, 37, 37, 37, 37, 37] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087593 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087593 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087593/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087593 Building REAL300004087594 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087594' /scratch/stefan/7774412/working/building/REAL300004087594 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087594 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087594/0 /scratch/stefan/7774412/working/building/REAL300004087594 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/741 `/scratch/stefan/7774412/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC=C(Br)C3=N2)S1) `REAL300004087594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087594 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC=C(Br)C3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 17, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 23, 23, 11, 1, 1, 1] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087594 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=CC=C(Br)C3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 17, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087594 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087594 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087594/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087594 Building REAL300004087595 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087595' /scratch/stefan/7774412/working/building/REAL300004087595 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087595 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087595/0 /scratch/stefan/7774412/working/building/REAL300004087595 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/742 `/scratch/stefan/7774412/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(COCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NO1) `REAL300004087595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087595 none CC1=CC(COCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 30, 8, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 69, 69, 69, 69, 69, 69, 30, 30, 2, 2, 2, 2, 2, 2, 2, 2] 85 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087595 none CC1=CC(COCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 30, 69, 69, 69, 69, 69, 69, 69, 85, 85, 85, 69, 69, 69, 1, 1, 2, 2, 2, 1, 9, 9, 69, 69, 69, 85, 85, 69, 69, 69] 85 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 333 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087595 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087595/1 /scratch/stefan/7774412/working/building/REAL300004087595 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/743 `/scratch/stefan/7774412/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(COCC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=NO1) `REAL300004087595.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087595/1/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: REAL300004087595 none CC1=CC(COCC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 156, 130, 99, 48, 13, 48, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 162, 162, 162, 162, 162, 162, 156, 156, 99, 99, 2, 2, 2, 2, 2] 201 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087595 none CC1=CC(COCC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 14, 19, 36, 36, 66, 162, 162, 162, 201, 201, 201, 162, 162, 162, 1, 1, 2, 2, 2, 1, 6, 6, 19, 19, 201, 201, 162, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087595 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087595 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087595/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087595/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087595 Building REAL300004087596 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087596' /scratch/stefan/7774412/working/building/REAL300004087596 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087596 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087596/0 /scratch/stefan/7774412/working/building/REAL300004087596 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/744 `/scratch/stefan/7774412/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CC(C)=C3N=C2)S1) `REAL300004087596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087596 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CC(C)=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 2, 2, 2, 1] 25 rigid atoms, others: [32, 33, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 35, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087596 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=CC(C)=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 5, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087596 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087596 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087596/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087596 Building REAL300004087597 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087597' /scratch/stefan/7774412/working/building/REAL300004087597 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087597 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087597/0 /scratch/stefan/7774412/working/building/REAL300004087597 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/745 `/scratch/stefan/7774412/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1) `REAL300004087597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087597 none CCCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [100, 82, 23, 23, 23, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 23, 23, 23, 100, 100, 100, 100, 100, 82, 82, 23, 2, 2, 2, 2, 2, 2, 23, 23, 23] 156 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 391 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087597 none CCCN1C=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 1, 1, 1, 1, 1, 13, 13, 17, 23, 23, 23, 40, 88, 88, 23, 23, 23, 1, 1, 1, 17, 17, 17, 17, 17, 9, 9, 1, 17, 40, 40, 23, 23, 23, 2, 2, 2] 156 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 21, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 388 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087597 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087597 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087597/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087597 Building REAL300004087598 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087598' /scratch/stefan/7774412/working/building/REAL300004087598 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087598 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087598/0 /scratch/stefan/7774412/working/building/REAL300004087598 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/746 `/scratch/stefan/7774412/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1N=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C) `REAL300004087598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087598 none CCCN1N=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 16, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 16, 49, 49, 49, 49, 49, 47, 46, 16, 2, 2, 2, 2, 2, 2, 16, 16, 16] 87 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087598 none CCCN1N=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 1, 1, 1, 1, 1, 1, 9, 9, 11, 16, 16, 16, 29, 45, 45, 15, 15, 15, 1, 1, 10, 10, 10, 9, 9, 5, 5, 1, 12, 29, 29, 16, 16, 16, 2, 2, 2] 87 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087598 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087598 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087598/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087598 Building REAL300004087599 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087599' /scratch/stefan/7774412/working/building/REAL300004087599 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087599 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087599/0 /scratch/stefan/7774412/working/building/REAL300004087599 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/747 `/scratch/stefan/7774412/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1) `REAL300004087599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087599 none COC1=CC=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [72, 22, 15, 43, 43, 15, 15, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 43, 43, 43, 72, 72, 72, 43, 43, 15, 15, 2, 2, 2, 2, 2, 2, 43, 43, 43, 43] 80 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 230 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087599 none COC1=CC=C(C=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 9, 9, 40, 40, 43, 43, 43, 43, 72, 80, 80, 43, 43, 43, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 42, 72, 72, 43, 43, 43, 2, 2, 2, 1] 80 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 327 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087599 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087599 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087599/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087599 Building REAL300004087600 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087600' /scratch/stefan/7774412/working/building/REAL300004087600 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087600 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087600/0 /scratch/stefan/7774412/working/building/REAL300004087600 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/748 `/scratch/stefan/7774412/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C(F)(F)F)=C2C)S1) `REAL300004087600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087600 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C(F)(F)F)=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 15, 15, 15, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 15, 15, 15, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 8, 1, 2, 2, 2] 15 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087600 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C(F)(F)F)=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 15, 15, 15, 1, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087600 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087600 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087600/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087600 Building REAL300004087601 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087601' /scratch/stefan/7774412/working/building/REAL300004087601 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087601 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087601/0 /scratch/stefan/7774412/working/building/REAL300004087601 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/749 `/scratch/stefan/7774412/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2C=CC=N2)S1) `REAL300004087601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087601 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 3, 3, 3, 3, 5, 5, 3, 1, 1, 1, 8, 8, 8] 11 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087601 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 9, 9, 9] 11 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087601 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC=C2N2C=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 11, 11, 11, 9, 9, 9, 8, 9, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 11, 11, 9, 8, 8, 8, 1, 1, 1] 11 rigid atoms, others: [33, 34, 35, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 25 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087601 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087601 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087601/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087601 Building REAL300004087602 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087602' /scratch/stefan/7774412/working/building/REAL300004087602 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087602 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087602/0 /scratch/stefan/7774412/working/building/REAL300004087602 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/750 `/scratch/stefan/7774412/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=N2)S1) `REAL300004087602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087602 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 56, 56, 56, 36, 36, 35, 15, 35, 3, 1, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 56, 56, 36, 15, 15, 1, 1, 1, 1] 56 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087602 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 34, 36, 36, 36, 36, 36, 1, 2, 2, 2, 2, 2, 2, 11, 11, 36, 36, 36, 36] 56 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087602 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087602/1 /scratch/stefan/7774412/working/building/REAL300004087602 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/751 `/scratch/stefan/7774412/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=N2)S1) `REAL300004087602.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087602/1/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: REAL300004087602 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 105, 54, 16, 54, 3, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 201, 201, 16, 16, 1, 1, 1, 1] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 517 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087602 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 39, 39, 96, 163, 172, 172, 172, 172, 172, 1, 2, 2, 2, 2, 2, 96, 96, 172, 172, 172, 172] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 480 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087602 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087602 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087602/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087602/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087602 Building REAL300004087603 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087603' /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087603 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087603/0 /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/752 `/scratch/stefan/7774412/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2CC(C)C)S1) `REAL300004087603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087603 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 11, 11, 11, 10, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3] 12 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 37 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087603 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 6, 9, 9, 10, 10, 10, 10, 10, 10, 10, 11, 11, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11] 12 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 55 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087603/1 /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/753 `/scratch/stefan/7774412/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2CC(C)C)S1) `REAL300004087603.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087603/1/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: REAL300004087603 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 6, 6, 6, 5, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 6 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087603 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 6 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087603/2 /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/754 `/scratch/stefan/7774412/working/3D/754' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2CC(C)C)S1) `REAL300004087603.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087603/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087603 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 21 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: REAL300004087603 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 27 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087603/3 /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/755 `/scratch/stefan/7774412/working/3D/755' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2CC(C)C)S1) `REAL300004087603.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087603/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087603 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087603 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+]2CC(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087603 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087603 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087603/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087603/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087603/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087603/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087603 Building REAL300004087604 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087604' /scratch/stefan/7774412/working/building/REAL300004087604 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087604 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087604/0 /scratch/stefan/7774412/working/building/REAL300004087604 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/756 `/scratch/stefan/7774412/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2CCC(CO)CC2)S1) `REAL300004087604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087604 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2CCC(CO)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 31, 36, 36, 18, 15, 15, 5, 15, 1, 1, 1, 1, 1, 1, 6, 1, 1, 18, 18, 18, 18, 31, 31, 15, 5, 5, 1, 1, 1, 1, 1, 6, 6, 18, 1, 1, 1, 1] 111 rigid atoms, others: [32, 33, 34, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 184 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087604 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2CCC(CO)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 18, 18, 18, 18, 25, 18, 18, 1, 2, 2, 2, 2, 2, 2, 12, 12, 18, 18, 18, 18, 18, 25, 25, 75, 18, 18, 18, 18] 111 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087604 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087604/1 /scratch/stefan/7774412/working/building/REAL300004087604 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/757 `/scratch/stefan/7774412/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2CCC(CO)CC2)S1) `REAL300004087604.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087604/1/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: REAL300004087604 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2CCC(CO)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 198, 201, 201, 153, 68, 30, 8, 30, 1, 1, 1, 1, 1, 1, 7, 1, 1, 153, 153, 153, 153, 198, 198, 8, 8, 1, 1, 1, 1, 1, 7, 7, 21, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087604 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2CCC(CO)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 38, 38, 88, 153, 153, 153, 153, 169, 153, 153, 1, 2, 2, 2, 2, 2, 88, 88, 153, 153, 153, 153, 153, 169, 169, 507, 153, 153, 153, 153] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 1042 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087604 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087604 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087604/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087604/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087604 Building REAL300004087605 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087605' /scratch/stefan/7774412/working/building/REAL300004087605 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087605 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087605/0 /scratch/stefan/7774412/working/building/REAL300004087605 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/758 `/scratch/stefan/7774412/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)CC2=CC=C(O)C=C2)S1) `REAL300004087605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087605 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)CC2=CC=C(O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 61, 61, 61, 34, 21, 21, 8, 21, 2, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 61, 61, 21, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 2, 1, 1] 122 rigid atoms, others: [38, 39, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087605 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)CC2=CC=C(O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 11, 11, 33, 34, 34, 33, 34, 34, 34, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 12, 12, 12, 33, 33, 34, 34, 67, 34, 34] 122 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087605 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087605/1 /scratch/stefan/7774412/working/building/REAL300004087605 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/759 `/scratch/stefan/7774412/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)CC2=CC=C(O)C=C2)S1) `REAL300004087605.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087605/1/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: REAL300004087605 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)CC2=CC=C(O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [147, 147, 147, 147, 201, 201, 201, 147, 64, 21, 7, 21, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 201, 201, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 2, 1, 1] 402 rigid atoms, others: [37, 38, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087605 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)CC2=CC=C(O)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 12, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 38, 38, 126, 126, 126, 147, 147, 147, 147, 147, 147, 147, 1, 2, 2, 2, 2, 2, 126, 126, 126, 126, 126, 126, 147, 147, 147, 147, 294, 147, 147] 402 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 878 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087605 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087605 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087605/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087605/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087605 Building REAL300004087606 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087606' /scratch/stefan/7774412/working/building/REAL300004087606 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087606 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087606/0 /scratch/stefan/7774412/working/building/REAL300004087606 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/760 `/scratch/stefan/7774412/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1) `REAL300004087606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087606 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 58, 58, 58, 31, 21, 18, 4, 18, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 4, 7, 7, 7, 31, 31, 31, 31, 58, 58, 21, 4, 1, 1, 1, 1, 1, 7, 7, 4, 7, 7, 7, 7] 60 rigid atoms, others: [34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 253 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087606 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 3, 3, 23, 31, 31, 23, 31, 31, 23, 31, 31, 23, 31, 31, 31, 1, 2, 2, 2, 3, 3, 2, 23, 31, 31, 23, 31, 31, 31, 31, 23, 31, 31, 31, 31] 60 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087606 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 59, 60, 60, 31, 21, 20, 6, 20, 1, 6, 7, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 59, 59, 21, 6, 7, 7, 6, 7, 7, 1, 1, 1, 1, 2, 2, 2] 60 rigid atoms, others: [39, 40, 41, 42, 12, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45]) total number of confs: 260 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087606 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087606/1 /scratch/stefan/7774412/working/building/REAL300004087606 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/761 `/scratch/stefan/7774412/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1) `REAL300004087606.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087606 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 194, 195, 195, 136, 41, 11, 4, 11, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 4, 6, 6, 6, 136, 136, 136, 136, 194, 194, 4, 1, 1, 1, 1, 1, 6, 6, 4, 6, 6, 6, 6] 201 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 555 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087606 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 61, 61, 122, 136, 136, 125, 136, 136, 122, 146, 146, 122, 146, 146, 146, 1, 2, 2, 2, 2, 2, 122, 136, 136, 132, 136, 136, 146, 146, 122, 146, 146, 146, 146] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 644 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087606 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2)C2=CC=CC=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 200, 201, 201, 146, 51, 13, 5, 13, 1, 5, 6, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 200, 200, 5, 6, 6, 5, 6, 6, 1, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [38, 39, 40, 41, 12, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) total number of confs: 555 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087606 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087606 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087606/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087606/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087606 Building REAL300004087607 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087607' /scratch/stefan/7774412/working/building/REAL300004087607 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087607 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087607/0 /scratch/stefan/7774412/working/building/REAL300004087607 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/762 `/scratch/stefan/7774412/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2CCCO2)S1) `REAL300004087607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087607 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 22, 22, 12, 9, 9, 5, 9, 1, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 9, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 94 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087607 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087607 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087607/1 /scratch/stefan/7774412/working/building/REAL300004087607 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/763 `/scratch/stefan/7774412/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2CCCO2)S1) `REAL300004087607.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087607/1/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: REAL300004087607 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 7, 6, 4, 6, 1, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 27 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087607 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 5, 8, 8, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087607 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087607 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087607/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087607/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087607 Building REAL300004087608 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087608' /scratch/stefan/7774412/working/building/REAL300004087608 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087608 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087608/0 /scratch/stefan/7774412/working/building/REAL300004087608 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/764 `/scratch/stefan/7774412/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=C(Cl)C=C2C)S1) `REAL300004087608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087608 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=C(Cl)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 16, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 4, 5, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 4, 4, 2, 2, 2, 2, 1, 1, 2, 2, 2] 5 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087608 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=C(Cl)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 16, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087608 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087608 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087608/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087608 Building REAL300004087609 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087609' /scratch/stefan/7774412/working/building/REAL300004087609 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087609 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087609/0 /scratch/stefan/7774412/working/building/REAL300004087609 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/765 `/scratch/stefan/7774412/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CC2(CCC2)C3)S1) `REAL300004087609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087609 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CC2(CCC2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 23, 23, 23, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087609 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CC2(CCC2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087609 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087609 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087609/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087609 Building REAL300004087610 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087610' /scratch/stefan/7774412/working/building/REAL300004087610 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087610 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087610/0 /scratch/stefan/7774412/working/building/REAL300004087610 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/766 `/scratch/stefan/7774412/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NC3=CC=NN32)S1) `REAL300004087610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087610 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 16, 32, 32, 8, 5, 5, 1, 5, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 16, 16, 5, 1, 7, 7, 7, 7, 7, 1, 1] 38 rigid atoms, others: [37, 38, 10, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087610 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 8, 8, 8, 28, 28, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 28, 28, 28, 28, 28, 8, 8] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087610 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 38, 38, 38, 28, 24, 24, 7, 24, 7, 7, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 28, 28, 28, 28, 38, 38, 24, 7, 1, 1, 1, 1, 1, 7, 7] 38 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38]) total number of confs: 120 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087610 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087610 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087610/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087610 Building REAL300004087611 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087611' /scratch/stefan/7774412/working/building/REAL300004087611 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087611 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087611/0 /scratch/stefan/7774412/working/building/REAL300004087611 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/767 `/scratch/stefan/7774412/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3SC=CC3=NC=C2)S1) `REAL300004087611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087611 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3SC=CC3=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 21, 21, 21, 13, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 21, 21, 11, 1, 1, 1, 1] 21 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087611 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3SC=CC3=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087611 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087611 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087611/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087611 Building REAL300004087612 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087612' /scratch/stefan/7774412/working/building/REAL300004087612 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087612 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087612/0 /scratch/stefan/7774412/working/building/REAL300004087612 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/768 `/scratch/stefan/7774412/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2COC3)S1) `REAL300004087612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087612 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2COC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 5, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 30, 30, 30, 18, 12, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 17, 18, 18, 18, 30, 30, 12, 1, 1, 1, 1, 1] 30 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087612 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2COC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 5, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087612 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087612 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087612/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087612 Building REAL300004087613 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087613' /scratch/stefan/7774412/working/building/REAL300004087613 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087613 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087613/0 /scratch/stefan/7774412/working/building/REAL300004087613 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/769 `/scratch/stefan/7774412/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087613 none C=CCC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [33, 29, 13, 13, 13, 5, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 33, 33, 33, 29, 29, 13, 5, 13, 13, 2, 2, 2, 2, 2, 2] 53 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087613 none C=CCC1=CC=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 11, 13, 13, 13, 25, 35, 35, 13, 13, 13, 19, 19, 19, 6, 6, 1, 1, 1, 1, 11, 25, 25, 13, 13, 13] 53 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087613 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087613 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087613/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087613 Building REAL300004087614 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087614' /scratch/stefan/7774412/working/building/REAL300004087614 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087614 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087614/0 /scratch/stefan/7774412/working/building/REAL300004087614 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/770 `/scratch/stefan/7774412/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)C3(C)C)S1) `REAL300004087614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087614 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 11, 11, 11, 21, 21, 21, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 21 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087614 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 39 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087614 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087614/1 /scratch/stefan/7774412/working/building/REAL300004087614 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/771 `/scratch/stefan/7774412/working/3D/771' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)C3(C)C)S1) `REAL300004087614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087614/1/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: REAL300004087614 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 37, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087614 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 67, 67, 148, 148, 148, 148, 148, 148, 148, 148, 1, 2, 2, 2, 2, 2, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087614 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087614 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087614/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087614/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087614 Building REAL300004087615 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087615' /scratch/stefan/7774412/working/building/REAL300004087615 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087615 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087615/0 /scratch/stefan/7774412/working/building/REAL300004087615 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/772 `/scratch/stefan/7774412/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC([N+](=O)[O-])=C1N) `REAL300004087615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087615 none COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC([N+](=O)[O-])=C1N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 17, 17, 17, 11, 2, 2, 2, 2, 2, 2, 11, 11, 11] 21 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087615 none COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC([N+](=O)[O-])=C1N NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 11, 11, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 19, 21, 21, 11, 11, 11, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 1, 7, 19, 19, 11, 11, 11, 1, 2, 2] 21 rigid atoms, others: [1, 2, 3, 4, 5, 35, 18, 19, 20, 23, 24, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087615 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087615 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087615/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087615 Building REAL300004087616 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087616' /scratch/stefan/7774412/working/building/REAL300004087616 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087616 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087616/0 /scratch/stefan/7774412/working/building/REAL300004087616 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/773 `/scratch/stefan/7774412/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(C)(F)F)CCOCC2)S1) `REAL300004087616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087616 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(C)(F)F)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 11, 11, 5, 3, 3, 1, 3, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087616 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(C)(F)F)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 5, 9, 9, 9, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087616 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087616/1 /scratch/stefan/7774412/working/building/REAL300004087616 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/774 `/scratch/stefan/7774412/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(C)(F)F)CCOCC2)S1) `REAL300004087616.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087616/1/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: REAL300004087616 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(C)(F)F)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 22 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087616 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(C)(F)F)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087616 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087616 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087616/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087616/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087616 Building REAL300004087617 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087617' /scratch/stefan/7774412/working/building/REAL300004087617 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087617 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087617/0 /scratch/stefan/7774412/working/building/REAL300004087617 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/775 `/scratch/stefan/7774412/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCC2)S1) `REAL300004087617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087617 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 20, 21, 21, 11, 7, 7, 1, 7, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 11, 11, 20, 20, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [35, 36, 37, 38, 39, 40, 10, 12, 13, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 91 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: REAL300004087617 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 11, 18, 18, 18, 18, 11, 11, 11, 1, 2, 2, 2, 2, 2, 3, 18, 18, 18, 18, 18, 18, 18, 11, 11, 11, 11, 11, 11] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087617 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 30, 30, 30, 18, 14, 14, 5, 14, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 30, 30, 14, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5] 30 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40]) total number of confs: 115 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087617 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087617/1 /scratch/stefan/7774412/working/building/REAL300004087617 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/776 `/scratch/stefan/7774412/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCC2)S1) `REAL300004087617.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087617 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 2, 2, 2, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087617 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087617 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 4 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39]) total number of confs: 11 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087617 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087617 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087617/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087617/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087617 Building REAL300004087618 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087618' /scratch/stefan/7774412/working/building/REAL300004087618 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087618 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087618/0 /scratch/stefan/7774412/working/building/REAL300004087618 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/777 `/scratch/stefan/7774412/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CCCO2)S1) `REAL300004087618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087618 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 28, 39, 39, 16, 10, 10, 1, 10, 1, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 16, 16, 16, 16, 28, 28, 10, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [39, 40, 41, 10, 43, 12, 13, 44, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087618 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 27, 27, 27, 27, 27, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 16, 16, 16, 16, 16, 16] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087618 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 47, 47, 47, 27, 17, 17, 4, 17, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 27, 27, 27, 27, 47, 47, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087618 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087618/1 /scratch/stefan/7774412/working/building/REAL300004087618 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/778 `/scratch/stefan/7774412/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CCCO2)S1) `REAL300004087618.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087618 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 14, 14, 14, 11, 5, 4, 1, 4, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 11, 11, 11, 11, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [38, 39, 40, 41, 10, 43, 12, 13, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087618 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 8, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087618 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 14, 14, 14, 11, 5, 4, 3, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 11, 11, 11, 11, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3] 14 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087618 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087618 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087618/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087618/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087618 Building REAL300004087619 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087619' /scratch/stefan/7774412/working/building/REAL300004087619 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087619 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087619/0 /scratch/stefan/7774412/working/building/REAL300004087619 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/779 `/scratch/stefan/7774412/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1) `REAL300004087619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087619 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 44, 45, 45, 24, 12, 12, 4, 12, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 24, 25, 25, 25, 44, 44, 12, 4, 1, 2, 2, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 45 rigid atoms, others: [34, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087619 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 12, 24, 24, 24, 24, 24, 24, 12, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 12, 24, 25, 25, 25, 24, 24, 24, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087619 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 24, 25, 25, 13, 7, 7, 2, 7, 1, 2, 6, 6, 6, 4, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 7, 2, 6, 7, 7, 7, 4, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [41, 42, 43, 12, 45, 46, 44, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087619 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087619/1 /scratch/stefan/7774412/working/building/REAL300004087619 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/780 `/scratch/stefan/7774412/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1) `REAL300004087619.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087619 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 135, 201, 201, 201, 135, 51, 10, 4, 10, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 135, 135, 135, 135, 201, 201, 4, 1, 2, 2, 2, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [33, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087619 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 12, 43, 43, 72, 135, 135, 135, 134, 135, 135, 72, 79, 79, 79, 79, 79, 1, 2, 2, 2, 3, 3, 72, 135, 135, 135, 135, 134, 135, 135, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79, 79] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087619 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 113, 127, 127, 79, 32, 9, 3, 9, 1, 3, 8, 8, 8, 6, 8, 8, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 113, 113, 3, 8, 9, 9, 9, 6, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 45, 46, 44, 48, 49, 50, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 397 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087619 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087619 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087619/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087619/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087619 Building REAL300004087620 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087620' /scratch/stefan/7774412/working/building/REAL300004087620 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087620 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087620/0 /scratch/stefan/7774412/working/building/REAL300004087620 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/781 `/scratch/stefan/7774412/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CC(F)=C2)S1) `REAL300004087620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087620 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 48, 67, 67, 26, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 26, 27, 27, 27, 48, 48, 14, 1, 2, 2, 2, 11, 11, 11, 11] 130 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 282 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: REAL300004087620 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 26, 26, 26, 26, 26, 26, 80, 80, 80, 80, 80, 80, 1, 2, 2, 2, 2, 2, 2, 26, 27, 27, 27, 80, 80, 80, 80] 130 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087620 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 130, 130, 130, 80, 58, 51, 11, 51, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 130, 130, 58, 11, 11, 11, 11, 1, 1, 1, 1] 130 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 484 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087620 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087620 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087620/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087620 Building REAL300004087621 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087621' /scratch/stefan/7774412/working/building/REAL300004087621 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087621 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087621/0 /scratch/stefan/7774412/working/building/REAL300004087621 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/782 `/scratch/stefan/7774412/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CSC=C2)=NO1) `REAL300004087621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087621 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CSC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 14, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 24, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 24, 24, 79, 79, 79, 79, 24, 24, 25, 25, 25, 2, 2, 2, 2, 2, 2, 79, 79, 79] 150 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 134 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087621 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CSC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 14, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 13, 24, 24, 25, 47, 47, 47, 24, 24, 24, 1, 1, 11, 11, 11, 11, 1, 1, 2, 2, 2, 13, 47, 47, 25, 25, 25, 11, 11, 11] 150 rigid atoms, others: [0, 1, 2, 3, 16, 17, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 210 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087621 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C2=CSC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 14, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 39, 39, 47, 79, 79, 79, 150, 150, 150, 79, 79, 79, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 47, 150, 150, 79, 79, 79, 1, 1, 1] 150 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 606 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087621 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087621 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087621/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087621 Building REAL300004087622 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087622' /scratch/stefan/7774412/working/building/REAL300004087622 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087622 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087622/0 /scratch/stefan/7774412/working/building/REAL300004087622 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/783 `/scratch/stefan/7774412/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(Cl)C3=CC=CN=C23)S1) `REAL300004087622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087622 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(Cl)C3=CC=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 45, 45, 45, 29, 25, 23, 7, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 45, 45, 25, 7, 7, 1, 1, 1, 1, 1] 45 rigid atoms, others: [33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 174 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087622 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(Cl)C3=CC=CN=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 16, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2, 2, 2, 2, 18, 18, 29, 29, 29, 29, 29] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087622 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087622 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087622/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087622 Building REAL300004087623 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087623' /scratch/stefan/7774412/working/building/REAL300004087623 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087623 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087623/0 /scratch/stefan/7774412/working/building/REAL300004087623 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/784 `/scratch/stefan/7774412/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CCC3)N=C2)S1) `REAL300004087623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087623 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 36, 36, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 6, 6, 6, 6, 6, 6, 6, 1] 70 rigid atoms, others: [38, 10, 12, 13, 14, 15, 16, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087623 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 39, 39, 39, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 39, 39, 39, 39, 39, 39, 39, 13] 70 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087623 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3CCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 70, 70, 70, 39, 31, 27, 6, 27, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 39, 39, 39, 39, 70, 70, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6] 70 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087623 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087623 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087623/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087623 Building REAL300004087624 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087624' /scratch/stefan/7774412/working/building/REAL300004087624 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087624 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087624/0 /scratch/stefan/7774412/working/building/REAL300004087624 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/785 `/scratch/stefan/7774412/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)SC2=N1) `REAL300004087624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087624 none CC1=CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087624 none CC1=CN2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)SC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 17, 17, 17, 9, 9, 8, 1, 1, 1, 2, 2, 2, 1, 1, 8, 17, 17, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 25, 26] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087624 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087624 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087624/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087624 Building REAL300004087625 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087625' /scratch/stefan/7774412/working/building/REAL300004087625 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087625 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087625/0 /scratch/stefan/7774412/working/building/REAL300004087625 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/786 `/scratch/stefan/7774412/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC(Cl)=C2)S1) `REAL300004087625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087625 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 89, 89, 89, 56, 47, 43, 11, 43, 1, 11, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 89, 89, 47, 11, 33, 1, 1, 1, 1] 267 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 381 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087625 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 267 conformations in input total number of sets (complete confs): 267 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 19, 20, 56, 56, 50, 56, 56, 56, 1, 2, 2, 2, 3, 3, 2, 20, 60, 56, 56, 56, 56] 267 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087625 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087625/1 /scratch/stefan/7774412/working/building/REAL300004087625 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/787 `/scratch/stefan/7774412/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC(Cl)=C2)S1) `REAL300004087625.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087625/1/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: REAL300004087625 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 201, 201, 201, 168, 90, 42, 11, 42, 1, 11, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 11, 33, 1, 1, 1, 1] 603 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087625 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 36, 36, 84, 84, 168, 168, 141, 168, 168, 168, 1, 2, 2, 2, 2, 2, 84, 252, 168, 168, 168, 168] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 832 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087625 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087625 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087625/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087625/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087625 Building REAL300004087626 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087626' /scratch/stefan/7774412/working/building/REAL300004087626 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087626 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087626/0 /scratch/stefan/7774412/working/building/REAL300004087626 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/788 `/scratch/stefan/7774412/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1) `REAL300004087626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087626 none CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [19, 13, 1, 13, 49, 49, 53, 74, 74, 74, 132, 166, 166, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 13, 53, 132, 132, 74, 74, 74, 1, 1, 1, 1] 167 rigid atoms, others: [2, 35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 718 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087626 none CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [38, 24, 4, 2, 4, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 24, 74, 74, 66, 74, 74, 74, 38, 38, 38, 38, 38, 24, 2, 3, 3, 2, 2, 2, 74, 74, 74, 74] 167 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 299 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087626 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087626/1 /scratch/stefan/7774412/working/building/REAL300004087626 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/789 `/scratch/stefan/7774412/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1) `REAL300004087626.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087626/1/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: REAL300004087626 none CCC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 1, 8, 19, 19, 51, 118, 118, 118, 165, 201, 201, 118, 118, 118, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 8, 165, 165, 118, 118, 118, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087626 none CCC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 67, 33, 13, 33, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 67, 118, 118, 110, 118, 118, 118, 88, 88, 88, 88, 88, 67, 2, 2, 2, 2, 2, 118, 118, 118, 118] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087626 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087626 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087626/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087626/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087626 Building REAL300004087627 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087627' /scratch/stefan/7774412/working/building/REAL300004087627 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087627 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087627/0 /scratch/stefan/7774412/working/building/REAL300004087627 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/790 `/scratch/stefan/7774412/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3=CC(C)=CC=C3S2)S1) `REAL300004087627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087627 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3=CC(C)=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 22, 22, 12, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 9, 1, 1, 1, 1, 2, 2, 2, 1, 1] 22 rigid atoms, others: [32, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 35, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 95 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087627 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3=CC(C)=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087627 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087627/1 /scratch/stefan/7774412/working/building/REAL300004087627 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/791 `/scratch/stefan/7774412/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CC3=CC(C)=CC=C3S2)S1) `REAL300004087627.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087627/1/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: REAL300004087627 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CC3=CC(C)=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 176, 176, 176, 138, 38, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 176, 176, 1, 1, 1, 1, 2, 2, 2, 1, 1] 176 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 22, 23, 24, 25, 26, 27]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087627 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CC3=CC(C)=CC=C3S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 58, 58, 138, 138, 138, 138, 138, 138, 138, 138, 138, 1, 2, 2, 2, 2, 2, 138, 138, 138, 138, 138, 138, 138, 138, 138] 176 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087627 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087627 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087627/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087627/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087627 Building REAL300004087628 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087628' /scratch/stefan/7774412/working/building/REAL300004087628 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087628 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087628/0 /scratch/stefan/7774412/working/building/REAL300004087628 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/792 `/scratch/stefan/7774412/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C3CCC3)C=C2)S1) `REAL300004087628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087628 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C3CCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 37, 37, 37, 19, 11, 11, 4, 11, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 19, 19, 19, 19, 37, 37, 11, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1] 129 rigid atoms, others: [32, 33, 41, 42, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087628 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C3CCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 9, 19, 19, 9, 9, 65, 65, 65, 19, 19, 1, 2, 2, 2, 3, 3, 2, 9, 9, 19, 19, 65, 65, 65, 65, 65, 65, 65, 19, 19] 129 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087628 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C(C3CCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 129, 129, 129, 65, 37, 37, 13, 37, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 65, 65, 65, 65, 129, 129, 37, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4] 129 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42]) total number of confs: 556 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087628 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087628 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087628/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087628 Building REAL300004087629 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087629' /scratch/stefan/7774412/working/building/REAL300004087629 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087629 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087629/0 /scratch/stefan/7774412/working/building/REAL300004087629 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/793 `/scratch/stefan/7774412/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=C3)=N2)S1) `REAL300004087629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087629 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 15, 25, 33, 33, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 14, 15, 15, 15, 25, 25, 11, 1, 1, 6, 6, 1, 6, 6] 39 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087629 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 27, 27, 14, 27, 27, 14, 1, 2, 2, 2, 2, 2, 2, 14, 15, 27, 27, 14, 27, 27] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087629 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 39, 39, 39, 28, 22, 22, 6, 22, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 27, 28, 28, 28, 39, 39, 22, 6, 6, 1, 1, 1, 1, 1] 39 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087629 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087629 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087629/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087629 Building REAL300004087630 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087630' /scratch/stefan/7774412/working/building/REAL300004087630 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087630 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087630/0 /scratch/stefan/7774412/working/building/REAL300004087630 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/794 `/scratch/stefan/7774412/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(F)(F)F)OC3=CC=CC=C32)S1) `REAL300004087630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087630 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(F)(F)F)OC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 15, 15, 15, 27, 27, 27, 15, 11, 9, 1, 9, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 11, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087630 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(F)(F)F)OC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 15, 15, 15, 12, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087630 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087630 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087630/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087630 Building REAL300004087631 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087631' /scratch/stefan/7774412/working/building/REAL300004087631 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087631 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087631/0 /scratch/stefan/7774412/working/building/REAL300004087631 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/795 `/scratch/stefan/7774412/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)C=C2C)S1) `REAL300004087631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087631 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 16, 16, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 1, 7, 7, 7, 7, 7, 1, 2, 2, 2] 28 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087631 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 18, 18, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 18, 18, 18, 18, 18, 7, 7, 7, 7] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087631 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 28, 28, 28, 18, 18, 18, 7, 18, 7, 7, 7, 1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 28, 28, 18, 7, 1, 1, 1, 1, 1, 7, 7, 7, 7] 28 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38]) total number of confs: 96 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087631 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087631 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087631/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087631 Building REAL300004087632 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087632' /scratch/stefan/7774412/working/building/REAL300004087632 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087632 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087632/0 /scratch/stefan/7774412/working/building/REAL300004087632 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/796 `/scratch/stefan/7774412/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CC=N2)CC3)S1) `REAL300004087632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087632 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CC=N2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 32, 47, 47, 17, 13, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 1, 17, 17, 17, 17, 32, 32, 13, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1] 72 rigid atoms, others: [32, 33, 34, 39, 40, 41, 10, 12, 13, 14, 15, 16, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087632 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CC=N2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 17, 17, 17, 17, 48, 48, 48, 48, 48, 17, 17, 1, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 48, 48, 48, 48, 17, 17, 17, 17] 72 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087632 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=CC=N2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 72, 72, 72, 48, 40, 37, 13, 37, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 48, 48, 48, 48, 72, 72, 40, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 72 rigid atoms, others: [35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 254 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087632 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087632 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087632/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087632 Building REAL300004087633 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087633' /scratch/stefan/7774412/working/building/REAL300004087633 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087633 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087633/0 /scratch/stefan/7774412/working/building/REAL300004087633 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/797 `/scratch/stefan/7774412/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)S1) `REAL300004087633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087633 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 12, 12, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 7, 7, 7, 7, 11, 11, 7, 1, 1, 4, 4, 4, 4] 13 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087633 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 8, 8, 7, 8, 8, 1, 2, 2, 2, 2, 2, 2, 7, 7, 8, 8, 8, 8] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087633 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 13, 13, 8, 8, 8, 4, 8, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 8, 4, 4, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087633 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087633 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087633/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087633 Building REAL300004087634 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087634' /scratch/stefan/7774412/working/building/REAL300004087634 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087634 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087634/0 /scratch/stefan/7774412/working/building/REAL300004087634 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/798 `/scratch/stefan/7774412/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=C(Br)C=CC3=N2)S1) `REAL300004087634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087634 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=C(Br)C=CC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 17, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 11, 11, 21, 21, 21, 11, 9, 9, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 21, 21, 9, 1, 1, 1] 21 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087634 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3C=C(Br)C=CC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 17, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 10, 11, 10, 11, 11, 11, 10, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087634 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087634 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087634/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087634 Building REAL300004087635 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087635' /scratch/stefan/7774412/working/building/REAL300004087635 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087635 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087635/0 /scratch/stefan/7774412/working/building/REAL300004087635 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/799 `/scratch/stefan/7774412/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(COC3=CC=CC=C3)=N2)S1) `REAL300004087635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087635 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(COC3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 9, 9, 15, 29, 29, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 9, 14, 14, 14, 14, 14, 14, 1, 8, 9, 9, 9, 15, 15, 6, 1, 9, 9, 14, 14, 14, 14, 14] 69 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087635 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(COC3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 9, 36, 41, 41, 41, 41, 41, 41, 8, 1, 2, 2, 2, 2, 2, 2, 9, 36, 36, 41, 41, 41, 41, 41] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087635 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(COC3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 12, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 69, 69, 69, 41, 32, 32, 14, 32, 14, 14, 14, 5, 2, 1, 1, 1, 1, 1, 1, 1, 14, 41, 41, 41, 41, 69, 69, 32, 14, 5, 5, 1, 1, 1, 1, 1] 69 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 263 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087635 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087635 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087635/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087635 Building REAL300004087636 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087636' /scratch/stefan/7774412/working/building/REAL300004087636 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087636 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087636/0 /scratch/stefan/7774412/working/building/REAL300004087636 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/800 `/scratch/stefan/7774412/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2)O1) `REAL300004087636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087636 none CC1=C(C)C2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 13, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 12, 13, 13, 13, 13, 13, 13, 12, 2, 2, 2, 2, 2, 2, 12] 23 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087636 none CC1=C(C)C2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 13, 12, 13, 23, 23, 23, 12, 12, 12, 1, 1, 2, 2, 2, 2, 2, 2, 1, 8, 23, 23, 13, 13, 13, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 36, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087636 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087636 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087636/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087636 Building REAL300004087637 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087637' /scratch/stefan/7774412/working/building/REAL300004087637 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087637 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087637/0 /scratch/stefan/7774412/working/building/REAL300004087637 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/801 `/scratch/stefan/7774412/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC(C)=C(Cl)C=C3N2)S1) `REAL300004087637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087637 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC(C)=C(Cl)C=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 16, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 25, 25, 25, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 24, 25, 8, 1, 1, 2, 2, 2, 1, 1] 25 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087637 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC(C)=C(Cl)C=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 16, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 13, 13, 13, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087637 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087637 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087637/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087637 Building REAL300004087638 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087638' /scratch/stefan/7774412/working/building/REAL300004087638 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087638 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087638/0 /scratch/stefan/7774412/working/building/REAL300004087638 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/802 `/scratch/stefan/7774412/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N(C)C2=C1) `REAL300004087638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087638 none COC1=CC=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [25, 19, 19, 19, 19, 19, 19, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 19, 19, 19, 19, 25, 25, 25, 19, 19, 19, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19] 37 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087638 none COC1=CC=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 19, 19, 19, 35, 37, 37, 19, 19, 19, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 14, 35, 35, 19, 19, 19, 2, 2, 2, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 40, 21, 22, 23, 24, 28, 29, 30] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087638 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087638 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087638/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087638 Building REAL300004087639 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087639' /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004087639 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087639/0 /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/803 `/scratch/stefan/7774412/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(=O)N1) `REAL300004087639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087639 none COCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 9, 9, 9, 9, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 9, 9, 19, 19, 19, 17, 17, 9, 2, 2, 2, 2, 2, 2, 9] 29 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087639 none COCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 15, 19, 19, 9, 9, 9, 1, 1, 1, 14, 14, 14, 6, 6, 1, 6, 15, 15, 9, 9, 9, 1] 29 rigid atoms, others: [2, 3, 4, 5, 6, 7, 35, 20, 21, 22, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087639/1 /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/804 `/scratch/stefan/7774412/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(=O)[N-]1) `REAL300004087639.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087639/1/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: REAL300004087639 none COCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 4, 4, 4, 10, 10, 10, 8, 8, 4, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087639 none COCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(=O)[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 9, 9, 4, 4, 4, 1, 1, 1, 9, 9, 9, 7, 7, 1, 4, 5, 5, 4, 4, 4] 15 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087639/2 /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/805 `/scratch/stefan/7774412/working/3D/805' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NC=C(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C(=O)N1) `REAL300004087639.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087639/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087639 none COCC1=NC=C(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 175, 97, 97, 97, 97, 46, 12, 46, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 97, 97, 97, 190, 190, 190, 175, 175, 97, 2, 2, 2, 2, 2, 97] 201 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087639 none COCC1=NC=C(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 1, 1, 1, 1, 1, 1, 12, 12, 37, 97, 97, 97, 120, 132, 132, 97, 97, 97, 1, 1, 1, 22, 22, 22, 6, 6, 1, 120, 120, 97, 97, 97, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 20, 21, 22, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087639 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087639 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087639/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087639/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087639/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087639 Building REAL300004087640 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087640' /scratch/stefan/7774412/working/building/REAL300004087640 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087640 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087640/0 /scratch/stefan/7774412/working/building/REAL300004087640 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/806 `/scratch/stefan/7774412/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C)C2=CC=C(C)C=C2)S1) `REAL300004087640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087640 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 21, 21, 21, 14, 14, 13, 8, 13, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 21, 21, 14, 8, 8, 5, 5, 5, 5, 1, 1, 2, 2, 2, 1, 1] 21 rigid atoms, others: [35, 36, 40, 41, 13, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087640 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 11, 11, 14, 14, 12, 12, 14, 14, 1, 2, 2, 2, 2, 2, 2, 7, 7, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087640 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087640 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087640/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087640 Building REAL300004087641 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087641' /scratch/stefan/7774412/working/building/REAL300004087641 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087641 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087641/0 /scratch/stefan/7774412/working/building/REAL300004087641 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/807 `/scratch/stefan/7774412/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C(F)(F)F)=C2)S1) `REAL300004087641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087641 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 10, 10, 10, 13, 13, 13, 10, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 10, 10, 10, 10, 13, 13, 9, 2, 2, 2, 1] 13 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087641 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087641 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087641 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087641/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087641 Building REAL300004087642 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087642' /scratch/stefan/7774412/working/building/REAL300004087642 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087642 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087642/0 /scratch/stefan/7774412/working/building/REAL300004087642 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/808 `/scratch/stefan/7774412/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C(C)O1) `REAL300004087642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087642 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [25, 17, 16, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 16, 17, 17, 17] 49 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087642 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 11, 11, 11, 16, 16, 17, 33, 35, 35, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 5, 5, 11, 33, 33, 17, 17, 17, 1, 2, 2, 2] 49 rigid atoms, others: [32, 1, 2, 3, 4, 17, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 167 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087642 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087642 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087642/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087642 Building REAL300004087643 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087643' /scratch/stefan/7774412/working/building/REAL300004087643 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087643 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087643/0 /scratch/stefan/7774412/working/building/REAL300004087643 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/809 `/scratch/stefan/7774412/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CC3(F)F)N=C2)S1) `REAL300004087643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087643 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CC3(F)F)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 9, 7, 1, 7, 1, 1, 1, 1, 11, 11, 11, 11, 1, 1, 13, 13, 13, 13, 23, 23, 9, 1, 11, 11, 11, 1] 92 rigid atoms, others: [33, 10, 12, 13, 14, 15, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087643 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CC3(F)F)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 55, 55, 55, 55, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 55, 55, 55, 13] 92 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087643 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CC3(F)F)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 15, 15, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 92, 92, 92, 55, 39, 38, 11, 38, 11, 11, 1, 1, 1, 1, 1, 1, 11, 11, 55, 55, 55, 55, 92, 92, 39, 11, 1, 1, 1, 11] 92 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33]) total number of confs: 342 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087643 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087643 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087643/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087643 Building REAL300004087644 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087644' /scratch/stefan/7774412/working/building/REAL300004087644 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087644 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087644/0 /scratch/stefan/7774412/working/building/REAL300004087644 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/810 `/scratch/stefan/7774412/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2C)C(C)C)S1) `REAL300004087644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087644 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2C)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 25, 25, 25, 15, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 15, 15, 15, 15, 25, 25, 8, 3, 1, 2, 2, 2, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 25 rigid atoms, others: [32, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 116 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087644 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC(C)=CC=C2C)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087644 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087644/1 /scratch/stefan/7774412/working/building/REAL300004087644 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/811 `/scratch/stefan/7774412/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2C)C(C)C)S1) `REAL300004087644.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087644/1/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: REAL300004087644 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2C)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 103, 103, 103, 73, 27, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 73, 73, 73, 73, 103, 103, 2, 1, 2, 2, 2, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 103 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 306 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087644 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC(C)=CC=C2C)C(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 5, 1, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 52, 52, 73, 73, 73, 73, 73, 73, 73, 73, 73, 78, 78, 1, 2, 2, 2, 2, 2, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 78, 78, 78, 78, 78, 78, 78] 103 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 293 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087644 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087644 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087644/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087644/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087644 Building REAL300004087645 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087645' /scratch/stefan/7774412/working/building/REAL300004087645 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087645 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087645/0 /scratch/stefan/7774412/working/building/REAL300004087645 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/812 `/scratch/stefan/7774412/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=C2)N=NN3C)S1) `REAL300004087645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087645 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=C2)N=NN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 17, 17, 17, 11, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 9, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087645 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=C2)N=NN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087645 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087645 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087645/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087645 Building REAL300004087646 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087646' /scratch/stefan/7774412/working/building/REAL300004087646 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087646 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087646/0 /scratch/stefan/7774412/working/building/REAL300004087646 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/813 `/scratch/stefan/7774412/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOC3)S2)S1) `REAL300004087646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087646 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOC3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [19, 20, 20, 20, 38, 52, 52, 20, 13, 13, 1, 13, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 20, 20, 20, 20, 38, 38, 13, 1, 12, 12, 12, 12, 12, 12, 12] 99 rigid atoms, others: [10, 12, 13, 14, 15, 16, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300004087646 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOC3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 20, 20, 20, 57, 57, 57, 57, 20, 1, 2, 2, 2, 2, 2, 2, 20, 57, 57, 57, 57, 57, 57, 57] 99 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087646 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOC3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 99, 99, 99, 57, 43, 43, 12, 43, 12, 12, 12, 1, 1, 1, 1, 1, 1, 12, 57, 57, 57, 57, 99, 99, 43, 12, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087646 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087646 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087646/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087646 Building REAL300004087647 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087647' /scratch/stefan/7774412/working/building/REAL300004087647 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087647 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087647/0 /scratch/stefan/7774412/working/building/REAL300004087647 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/814 `/scratch/stefan/7774412/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=NN(C)C=C2)S1) `REAL300004087647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087647 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 20, 31, 31, 13, 13, 10, 1, 10, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 13, 20, 20, 13, 1, 1, 11, 11, 11, 11, 11] 47 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087647 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 45, 45, 45, 45, 45, 1, 2, 2, 2, 3, 3, 2, 13, 13, 45, 45, 45, 45, 45] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087647 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 47, 47, 47, 45, 45, 40, 11, 40, 11, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 47, 47, 45, 11, 11, 2, 2, 2, 1, 1] 47 rigid atoms, others: [35, 36, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 139 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087647 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087647 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087647/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087647 Building REAL300004087648 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087648' /scratch/stefan/7774412/working/building/REAL300004087648 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087648 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087648/0 /scratch/stefan/7774412/working/building/REAL300004087648 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/815 `/scratch/stefan/7774412/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COCCC2=CC=C(Cl)S2)S1) `REAL300004087648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087648 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCCC2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 201, 201, 201, 165, 165, 165, 164, 165, 73, 19, 8, 1, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 201, 201, 165, 165, 165, 19, 19, 8, 8, 1, 1] 201 rigid atoms, others: [35, 36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 780 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: REAL300004087648 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCCC2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 2, 8, 32, 70, 165, 165, 165, 165, 165, 1, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 70, 70, 165, 165] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 464 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087648 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087648/1 /scratch/stefan/7774412/working/building/REAL300004087648 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/816 `/scratch/stefan/7774412/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCCC2=CC=C(Cl)S2)S1) `REAL300004087648.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087648/1/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: REAL300004087648 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCCC2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 201, 201, 201, 184, 143, 113, 75, 113, 37, 14, 6, 1, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 201, 201, 76, 76, 14, 14, 6, 6, 1, 1] 201 rigid atoms, others: [34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 634 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087648 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCCC2=CC=C(Cl)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 16, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 6, 19, 19, 33, 57, 119, 170, 184, 184, 184, 184, 184, 1, 2, 2, 2, 2, 2, 33, 33, 119, 119, 170, 170, 184, 184] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087648 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087648 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087648/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087648/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087648 Building REAL300004087649 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087649' /scratch/stefan/7774412/working/building/REAL300004087649 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087649 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087649/0 /scratch/stefan/7774412/working/building/REAL300004087649 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/817 `/scratch/stefan/7774412/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC=N2)S1) `REAL300004087649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087649 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 21, 21, 37, 48, 48, 21, 15, 11, 1, 11, 1, 1, 1, 8, 8, 1, 1, 1, 20, 21, 21, 21, 37, 37, 16, 8, 8, 8, 8, 8, 1] 64 rigid atoms, others: [32, 10, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL300004087649 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 21, 39, 39, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 21] 64 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087649 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CC3)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 64, 64, 64, 39, 33, 32, 8, 32, 8, 1, 1, 1, 1, 8, 8, 8, 39, 39, 39, 39, 64, 64, 33, 1, 1, 1, 1, 1, 8] 64 rigid atoms, others: [13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32]) total number of confs: 237 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087649 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087649 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087649/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087649 Building REAL300004087650 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087650' /scratch/stefan/7774412/working/building/REAL300004087650 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087650 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087650/0 /scratch/stefan/7774412/working/building/REAL300004087650 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/818 `/scratch/stefan/7774412/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)O1) `REAL300004087650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087650 none CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [46, 23, 23, 23, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 23, 23, 23, 46, 46, 46, 46, 46, 23, 2, 2, 2, 2, 2, 2, 23, 23, 23] 78 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087650 none CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 12, 12, 15, 23, 23, 23, 45, 59, 59, 23, 23, 23, 1, 1, 1, 9, 9, 9, 8, 8, 1, 15, 45, 45, 23, 23, 23, 2, 2, 2] 78 rigid atoms, others: [1, 2, 3, 4, 5, 18, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 277 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087650 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087650 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087650/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087650 Building REAL300004087651 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087651' /scratch/stefan/7774412/working/building/REAL300004087651 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087651 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087651/0 /scratch/stefan/7774412/working/building/REAL300004087651 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/819 `/scratch/stefan/7774412/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=C(C(F)(F)F)C3=C2CCC3)S1) `REAL300004087651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087651 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=C(C(F)(F)F)C3=C2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 18, 18, 18, 13, 13, 12, 7, 12, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 13, 13, 13, 13, 18, 18, 13, 7, 7, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087651 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=C(C(F)(F)F)C3=C2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 6, 6, 13, 13, 13, 13, 13, 13] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087651 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087651/1 /scratch/stefan/7774412/working/building/REAL300004087651 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/820 `/scratch/stefan/7774412/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=C(C(F)(F)F)C3=C2CCC3)S1) `REAL300004087651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087651/1/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: REAL300004087651 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=C(C(F)(F)F)C3=C2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 201, 201, 201, 158, 75, 26, 6, 26, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 158, 158, 158, 158, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087651 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=C(C(F)(F)F)C3=C2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 1, 5, 15, 15, 15, 1, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 44, 44, 119, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 1, 2, 2, 2, 2, 2, 119, 119, 158, 158, 158, 158, 158, 158] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 514 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087651 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087651 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087651/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087651/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087651 Building REAL300004087652 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087652' /scratch/stefan/7774412/working/building/REAL300004087652 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087652 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087652/0 /scratch/stefan/7774412/working/building/REAL300004087652 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/821 `/scratch/stefan/7774412/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3=NN(C)C=C3)=C2)S1) `REAL300004087652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087652 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3=NN(C)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 8, 8, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 26, 37, 37, 15, 12, 10, 1, 10, 1, 1, 1, 1, 1, 10, 10, 11, 10, 10, 1, 15, 16, 16, 16, 26, 26, 12, 11, 11, 11, 10, 11, 1] 49 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087652 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3=NN(C)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 8, 8, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 32, 32, 33, 32, 32, 15, 1, 2, 2, 2, 2, 2, 2, 33, 33, 33, 33, 33, 15] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087652 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC(C3=NN(C)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 8, 8, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 32, 49, 49, 49, 32, 26, 26, 11, 27, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 33, 33, 33, 33, 49, 48, 26, 2, 2, 2, 1, 1, 11] 49 rigid atoms, others: [33, 34, 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, 35]) total number of confs: 186 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087652 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087652 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087652/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087652 Building REAL300004087653 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087653' /scratch/stefan/7774412/working/building/REAL300004087653 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087653 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087653/0 /scratch/stefan/7774412/working/building/REAL300004087653 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/822 `/scratch/stefan/7774412/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(C)(C)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087653 none CCC(F)(F)C(C)(C)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [16, 12, 8, 16, 16, 2, 8, 8, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 17, 17, 17, 16, 16, 8, 8, 8, 9, 9, 9, 2, 2, 2, 2, 2, 2] 33 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087653 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087653/1 /scratch/stefan/7774412/working/building/REAL300004087653 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/823 `/scratch/stefan/7774412/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(C)(C)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087653.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087653 none CCC(F)(F)C(C)(C)C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 115, 139, 153, 153, 55, 139, 139, 13, 55, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 153, 153, 153, 153, 153, 139, 139, 139, 139, 139, 139, 2, 2, 2, 2, 2] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 848 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087653 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087653 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087653/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087653/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087653 Building REAL300004087654 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087654' /scratch/stefan/7774412/working/building/REAL300004087654 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087654 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087654/0 /scratch/stefan/7774412/working/building/REAL300004087654 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/824 `/scratch/stefan/7774412/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COCCC2=CC=CS2)S1) `REAL300004087654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087654 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCCC2=CC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 198, 198, 198, 146, 144, 146, 138, 146, 54, 13, 5, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 198, 198, 146, 138, 138, 13, 13, 5, 5, 1, 1, 1] 198 rigid atoms, others: [34, 35, 36, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087654 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCCC2=CC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 12, 34, 64, 146, 146, 146, 146, 1, 2, 2, 2, 2, 2, 2, 6, 6, 34, 34, 64, 64, 146, 146, 146] 198 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087654 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087654/1 /scratch/stefan/7774412/working/building/REAL300004087654 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/825 `/scratch/stefan/7774412/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCCC2=CC=CS2)S1) `REAL300004087654.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087654/1/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: REAL300004087654 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCCC2=CC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 201, 201, 201, 177, 124, 80, 47, 80, 21, 7, 3, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 201, 201, 47, 47, 7, 7, 3, 3, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 581 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087654 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCCC2=CC=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 26, 26, 42, 69, 131, 167, 177, 177, 177, 177, 1, 2, 2, 2, 2, 2, 42, 42, 131, 131, 167, 167, 177, 177, 177] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087654 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087654 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087654/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087654/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087654 Building REAL300004087655 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087655' /scratch/stefan/7774412/working/building/REAL300004087655 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087655 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087655/0 /scratch/stefan/7774412/working/building/REAL300004087655 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/826 `/scratch/stefan/7774412/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=C(C)C=C(Br)C=C2C)S1) `REAL300004087655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087655 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=C(C)C=C(Br)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 5, 1, 1, 17, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2] 7 rigid atoms, others: [34, 35, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087655 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=C(C)C=C(Br)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 5, 1, 1, 17, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 3, 3, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 29 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087655 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087655 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087655/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087655 Building REAL300004087656 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087656' /scratch/stefan/7774412/working/building/REAL300004087656 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087656 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087656/0 /scratch/stefan/7774412/working/building/REAL300004087656 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/827 `/scratch/stefan/7774412/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3C=CC=C(Br)C3=N2)S1) `REAL300004087656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087656 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3C=CC=C(Br)C3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 18, 19, 8, 1, 1, 1, 1] 19 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087656 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN3C=CC=C(Br)C3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 17, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 12, 12, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 12] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087656 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087656 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087656/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087656 Building REAL300004087657 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087657' /scratch/stefan/7774412/working/building/REAL300004087657 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087657 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087657/0 /scratch/stefan/7774412/working/building/REAL300004087657 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/828 `/scratch/stefan/7774412/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCCOC1) `REAL300004087657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087657 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 1, 8, 11, 11, 11, 17, 17, 17, 28, 28, 28, 17, 17, 17, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 11, 28, 28, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [32, 33, 2, 35, 36, 37, 38, 39, 40, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087657 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 3, 2, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 8, 17, 17, 17, 17, 17, 10, 10, 10, 8, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 17] 28 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087657 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087657/1 /scratch/stefan/7774412/working/building/REAL300004087657 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/829 `/scratch/stefan/7774412/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1CCCOC1) `REAL300004087657.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087657/1/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: REAL300004087657 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 1, 10, 22, 22, 55, 148, 148, 148, 201, 201, 201, 148, 148, 148, 1, 1, 1, 1, 1, 1, 17, 17, 17, 10, 201, 201, 148, 148, 148, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 36, 37, 38, 39, 34, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 572 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087657 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1CCCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 88, 51, 12, 51, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 88, 148, 148, 148, 148, 148, 106, 106, 106, 88, 2, 2, 2, 2, 2, 148, 148, 148, 148, 148, 148, 148, 148, 148] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087657 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087657 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087657/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087657/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087657 Building REAL300004087658 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087658' /scratch/stefan/7774412/working/building/REAL300004087658 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087658 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087658/0 /scratch/stefan/7774412/working/building/REAL300004087658 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/830 `/scratch/stefan/7774412/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CC=C2)CC3)S1) `REAL300004087658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087658 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CC=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 19, 19, 9, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 9, 9, 9, 9, 17, 17, 6, 1, 1, 6, 6, 2, 6, 6, 1, 1, 1, 1] 27 rigid atoms, others: [33, 34, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087658 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CC=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 16, 16, 14, 16, 16, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 16, 16, 14, 16, 16, 9, 9, 9, 9] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087658 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CC=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 27, 27, 27, 16, 12, 10, 6, 10, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 27, 27, 12, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 6] 27 rigid atoms, others: [35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087658 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087658 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087658/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087658 Building REAL300004087659 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087659' /scratch/stefan/7774412/working/building/REAL300004087659 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087659 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087659/0 /scratch/stefan/7774412/working/building/REAL300004087659 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/831 `/scratch/stefan/7774412/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)C=CN3C)S1) `REAL300004087659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087659 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)C=CN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 35, 22, 23, 24, 25, 26, 27, 28, 36]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087659 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C(=C2)C=CN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087659 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087659 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087659/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087659 Building REAL300004087660 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087660' /scratch/stefan/7774412/working/building/REAL300004087660 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087660 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087660/0 /scratch/stefan/7774412/working/building/REAL300004087660 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/832 `/scratch/stefan/7774412/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(F)C=C3OC=CC3=C2)S1) `REAL300004087660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087660 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(F)C=C3OC=CC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 8, 1, 1, 1, 1] 17 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087660 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(F)C=C3OC=CC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 15, 1, 1, 12, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087660 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087660 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087660/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087660 Building REAL300004087661 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087661' /scratch/stefan/7774412/working/building/REAL300004087661 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087661 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087661/0 /scratch/stefan/7774412/working/building/REAL300004087661 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/833 `/scratch/stefan/7774412/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=CS2)S1) `REAL300004087661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087661 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 42, 51, 51, 22, 14, 12, 1, 12, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 1, 1, 22, 23, 23, 23, 42, 42, 14, 1, 3, 3, 3, 3, 1] 51 rigid atoms, others: [36, 10, 12, 13, 14, 15, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087661 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 22, 41, 41, 23, 41, 41, 41, 22, 22, 1, 2, 2, 2, 2, 2, 2, 22, 41, 41, 41, 41, 22] 51 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087661 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(F)C=C3)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 51, 51, 51, 41, 27, 25, 3, 25, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 41, 41, 51, 51, 27, 3, 1, 1, 1, 1, 3] 51 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 148 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087661 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087661 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087661/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087661 Building REAL300004087662 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087662' /scratch/stefan/7774412/working/building/REAL300004087662 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087662 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087662/0 /scratch/stefan/7774412/working/building/REAL300004087662 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/834 `/scratch/stefan/7774412/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CCCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087662 none CCC(C)(C)CCCC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [55, 44, 16, 44, 44, 14, 10, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 63, 63, 63, 63, 63, 49, 45, 49, 49, 49, 45, 16, 16, 16, 16, 10, 10, 2, 2, 2, 2, 2, 2] 115 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 398 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087662 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087662 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087662/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087662 Building REAL300004087663 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087663' /scratch/stefan/7774412/working/building/REAL300004087663 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087663 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087663/0 /scratch/stefan/7774412/working/building/REAL300004087663 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/835 `/scratch/stefan/7774412/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(C)C=C2)S1) `REAL300004087663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087663 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 16, 16, 8, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 8, 8, 8, 8, 15, 15, 8, 1, 1, 4, 4, 4, 4, 4, 4, 4] 17 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087663 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 10, 10, 8, 8, 10, 10, 1, 2, 2, 2, 2, 2, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087663 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 17, 17, 17, 10, 10, 10, 4, 10, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 4, 4, 1, 1, 2, 2, 2, 1, 1] 17 rigid atoms, others: [33, 34, 38, 39, 15, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 73 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087663 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087663 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087663/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087663 Building REAL300004087664 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087664' /scratch/stefan/7774412/working/building/REAL300004087664 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087664 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087664/0 /scratch/stefan/7774412/working/building/REAL300004087664 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/836 `/scratch/stefan/7774412/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3N=NC(C)=C(C)C3=C2)S1) `REAL300004087664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087664 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3N=NC(C)=C(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 2, 2, 2, 2, 2, 2, 1] 25 rigid atoms, others: [32, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087664 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3N=NC(C)=C(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 5, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 44 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087664 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087664 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087664/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087664 Building REAL300004087665 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087665' /scratch/stefan/7774412/working/building/REAL300004087665 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087665 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087665/0 /scratch/stefan/7774412/working/building/REAL300004087665 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/837 `/scratch/stefan/7774412/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCNS2(=O)=O)S1) `REAL300004087665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087665 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 12, 12, 12, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087665 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8] 12 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087665 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087665/1 /scratch/stefan/7774412/working/building/REAL300004087665 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/838 `/scratch/stefan/7774412/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCNS2(=O)=O)S1) `REAL300004087665.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087665/1/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: REAL300004087665 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 60, 60, 60, 50, 20, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25]) total number of confs: 140 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087665 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 38, 38, 50, 50, 50, 50, 50, 50, 50, 1, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50] 60 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087665 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087665 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087665/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087665/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087665 Building REAL300004087666 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087666' /scratch/stefan/7774412/working/building/REAL300004087666 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087666 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087666/0 /scratch/stefan/7774412/working/building/REAL300004087666 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/839 `/scratch/stefan/7774412/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3OC(C)C(C)C3=C2)S1) `REAL300004087666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087666 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3OC(C)C(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 24, 24, 24, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 9, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1] 24 rigid atoms, others: [32, 36, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 37, 38, 39]) total number of confs: 109 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087666 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3OC(C)C(C)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087666 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087666 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087666/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087666 Building REAL300004087667 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087667' /scratch/stefan/7774412/working/building/REAL300004087667 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087667 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087667/0 /scratch/stefan/7774412/working/building/REAL300004087667 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/840 `/scratch/stefan/7774412/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=CNC2=C1) `REAL300004087667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087667 none COC1=CC=C2C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=CNC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [71, 55, 55, 55, 55, 55, 15, 4, 3, 4, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 55, 55, 55, 55, 71, 71, 71, 55, 55, 15, 15, 3, 2, 2, 2, 2, 2, 55, 55, 55] 101 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087667 none COC1=CC=C2C(CC(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=CNC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 8, 53, 53, 53, 55, 55, 55, 101, 101, 101, 55, 55, 55, 1, 1, 1, 1, 3, 3, 3, 1, 1, 8, 8, 53, 101, 101, 55, 55, 55, 1, 1, 1] 101 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 40, 39, 21, 22, 23, 24, 38, 28, 29] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087667 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087667 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087667/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087667 Building REAL300004087668 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087668' /scratch/stefan/7774412/working/building/REAL300004087668 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087668 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087668/0 /scratch/stefan/7774412/working/building/REAL300004087668 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/841 `/scratch/stefan/7774412/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN(CC3=CC=CC=C3)N=C2)S1) `REAL300004087668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087668 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN(CC3=CC=CC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 53, 55, 55, 29, 21, 21, 8, 21, 1, 1, 1, 1, 1, 8, 10, 10, 9, 10, 10, 1, 1, 29, 29, 29, 29, 53, 53, 21, 8, 8, 1, 8, 8, 10, 10, 9, 10, 10, 1] 201 rigid atoms, others: [34, 42, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087668 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN(CC3=CC=CC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 7, 29, 29, 29, 112, 118, 118, 115, 118, 118, 29, 29, 1, 2, 2, 2, 3, 3, 2, 7, 7, 29, 112, 112, 118, 118, 116, 118, 118, 29] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 412 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087668 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN(CC3=CC=CC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 201, 201, 201, 118, 105, 105, 48, 105, 10, 10, 10, 3, 1, 1, 1, 1, 1, 1, 1, 10, 10, 118, 118, 118, 118, 201, 201, 105, 48, 48, 10, 3, 3, 1, 1, 1, 1, 1, 10] 201 rigid atoms, others: [37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42]) total number of confs: 853 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087668 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087668 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087668/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087668 Building REAL300004087669 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087669' /scratch/stefan/7774412/working/building/REAL300004087669 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087669 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087669/0 /scratch/stefan/7774412/working/building/REAL300004087669 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/842 `/scratch/stefan/7774412/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)O1) `REAL300004087669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087669 none CCCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [117, 90, 22, 22, 22, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 22, 22, 22, 117, 117, 117, 117, 117, 90, 90, 22, 2, 2, 2, 2, 2, 2, 22, 22, 22] 182 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 486 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087669 none CCCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [20, 8, 1, 1, 1, 1, 1, 12, 12, 15, 22, 22, 22, 43, 94, 94, 22, 22, 22, 1, 1, 1, 20, 20, 20, 20, 20, 8, 8, 1, 15, 43, 43, 22, 22, 22, 2, 2, 2] 182 rigid atoms, others: [2, 3, 4, 5, 6, 19, 20, 21, 29] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 436 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087669 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087669 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087669/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087669 Building REAL300004087670 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087670' /scratch/stefan/7774412/working/building/REAL300004087670 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087670 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087670/0 /scratch/stefan/7774412/working/building/REAL300004087670 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/843 `/scratch/stefan/7774412/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=N2)C=CN3C)S1) `REAL300004087670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087670 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=N2)C=CN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 25, 25, 25, 17, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 25, 25, 13, 1, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 35, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087670 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C(=CC=N2)C=CN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087670 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087670 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087670/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087670 Building REAL300004087671 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087671' /scratch/stefan/7774412/working/building/REAL300004087671 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087671 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087671/0 /scratch/stefan/7774412/working/building/REAL300004087671 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/844 `/scratch/stefan/7774412/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)ON=C2C2=CC=CC=C2)S1) `REAL300004087671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087671 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)ON=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [22, 23, 23, 23, 45, 53, 53, 23, 14, 12, 1, 12, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 1, 6, 6, 22, 23, 23, 23, 45, 45, 14, 2, 2, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6] 73 rigid atoms, others: [10, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 244 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087671 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)ON=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 23, 23, 23, 23, 22, 23, 23, 23, 41, 41, 24, 41, 41, 1, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 41, 41, 26, 41, 41] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 140 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087671 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)ON=C2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 8, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 73, 73, 73, 41, 26, 24, 6, 24, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 73, 73, 26, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1] 73 rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 283 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087671 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087671 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087671/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087671 Building REAL300004087672 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087672' /scratch/stefan/7774412/working/building/REAL300004087672 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087672 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087672/0 /scratch/stefan/7774412/working/building/REAL300004087672 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/845 `/scratch/stefan/7774412/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCC2)S1) `REAL300004087672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087672 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 29, 29, 29, 15, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 15, 15, 15, 15, 29, 29, 8, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4] 29 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 132 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087672 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 1, 2, 2, 2, 3, 3, 2, 15, 15, 15, 15, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16, 16] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087672 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 29, 29, 16, 10, 10, 3, 10, 1, 3, 4, 4, 3, 4, 4, 4, 1, 1, 1, 1, 1, 16, 16, 16, 16, 29, 29, 10, 3, 4, 4, 3, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [40, 41, 42, 43, 12, 45, 46, 44, 48, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087672 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087672/1 /scratch/stefan/7774412/working/building/REAL300004087672 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/846 `/scratch/stefan/7774412/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCC2)S1) `REAL300004087672.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087672 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 125, 125, 125, 91, 33, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 91, 91, 91, 91, 125, 125, 2, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 125 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 344 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087672 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 51, 51, 91, 91, 91, 91, 91, 91, 91, 91, 100, 100, 100, 100, 1, 2, 2, 2, 2, 2, 91, 91, 91, 91, 91, 91, 91, 91, 100, 100, 100, 100, 100, 100, 100, 100, 100] 125 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 385 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087672 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 125, 125, 125, 100, 42, 11, 2, 11, 1, 2, 3, 3, 2, 3, 3, 3, 1, 1, 1, 1, 1, 100, 100, 100, 100, 125, 125, 2, 3, 3, 2, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 125 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 46, 44, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087672 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087672 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087672/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087672/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087672 Building REAL300004087673 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087673' /scratch/stefan/7774412/working/building/REAL300004087673 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087673 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087673/0 /scratch/stefan/7774412/working/building/REAL300004087673 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/847 `/scratch/stefan/7774412/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CCC3)OC=N2)S1) `REAL300004087673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087673 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CCC3)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 32, 46, 46, 19, 14, 10, 1, 10, 1, 1, 1, 7, 7, 7, 1, 1, 1, 19, 19, 19, 19, 32, 32, 14, 7, 7, 7, 7, 7, 7, 7, 1] 59 rigid atoms, others: [35, 10, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087673 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CCC3)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 19, 39, 39, 39, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 19] 59 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087673 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C3CCC3)OC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 12, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 59, 59, 59, 39, 30, 27, 7, 27, 7, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 39, 39, 59, 59, 30, 1, 1, 1, 1, 1, 1, 1, 7] 59 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35]) total number of confs: 210 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087673 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087673 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087673/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087673 Building REAL300004087674 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087674' /scratch/stefan/7774412/working/building/REAL300004087674 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087674 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087674/0 /scratch/stefan/7774412/working/building/REAL300004087674 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/848 `/scratch/stefan/7774412/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)S1) `REAL300004087674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087674 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 22, 23, 23, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087674 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H]3C[C@@H]2CO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087674 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087674 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087674/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087674 Building REAL300004087675 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087675' /scratch/stefan/7774412/working/building/REAL300004087675 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087675 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087675/0 /scratch/stefan/7774412/working/building/REAL300004087675 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/849 `/scratch/stefan/7774412/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC(C(C)(C)C)=C2)S1) `REAL300004087675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087675 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC(C(C)(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 23, 23, 9, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 45 rigid atoms, others: [40, 10, 12, 13, 14, 15, 16, 17, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087675 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC(C(C)(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 25, 25, 25, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087675 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087675 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087675/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087675 Building REAL300004087676 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087676' /scratch/stefan/7774412/working/building/REAL300004087676 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087676 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087676/0 /scratch/stefan/7774412/working/building/REAL300004087676 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/850 `/scratch/stefan/7774412/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC(F)(F)F)=C2C)S1) `REAL300004087676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087676 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC(F)(F)F)=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 23, 38, 38, 13, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1, 13, 13, 13, 13, 23, 23, 13, 1, 1, 1, 2, 2, 2] 65 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 178 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087676 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC(F)(F)F)=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 43, 45, 45, 45, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087676 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087676 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087676/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087676 Building REAL300004087677 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087677' /scratch/stefan/7774412/working/building/REAL300004087677 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087677 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087677/0 /scratch/stefan/7774412/working/building/REAL300004087677 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/851 `/scratch/stefan/7774412/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=CC(C(F)(F)F)=C2)S1) `REAL300004087677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087677 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=CC(C(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 201, 201, 201, 119, 90, 79, 13, 79, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 201, 201, 90, 13, 13, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 790 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: REAL300004087677 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=CC(C(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 105, 119, 37, 119, 119, 119, 119, 119, 119, 1, 2, 2, 2, 2, 2, 2, 24, 25, 25, 25, 119, 119, 43, 119] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 414 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087677 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087677/1 /scratch/stefan/7774412/working/building/REAL300004087677 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/852 `/scratch/stefan/7774412/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=CC(C(F)(F)F)=C2)S1) `REAL300004087677.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087677/1/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: REAL300004087677 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=CC(C(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 201, 201, 201, 160, 67, 28, 11, 28, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 201, 201, 11, 11, 11, 11, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 514 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087677 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=CC(C(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 36, 36, 74, 74, 160, 160, 114, 160, 160, 160, 160, 160, 160, 1, 2, 2, 2, 2, 2, 74, 74, 74, 74, 160, 160, 118, 160] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 538 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087677 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087677 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087677/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087677/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087677 Building REAL300004087678 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087678' /scratch/stefan/7774412/working/building/REAL300004087678 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087678 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087678/0 /scratch/stefan/7774412/working/building/REAL300004087678 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/853 `/scratch/stefan/7774412/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC23CCOCC3)S1) `REAL300004087678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087678 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC23CCOCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087678 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC23CCOCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087678 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087678 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087678/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087678 Building REAL300004087679 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087679' /scratch/stefan/7774412/working/building/REAL300004087679 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087679 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087679/0 /scratch/stefan/7774412/working/building/REAL300004087679 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/854 `/scratch/stefan/7774412/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C(F)(F)F) `REAL300004087679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087679 none COC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13] 25 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087679 none COC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 25, 25, 13, 13, 13, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 9, 25, 25, 13, 13, 13, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 28, 35] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087679 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087679 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087679/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087679 Building REAL300004087680 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087680' /scratch/stefan/7774412/working/building/REAL300004087680 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087680 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087680/0 /scratch/stefan/7774412/working/building/REAL300004087680 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/855 `/scratch/stefan/7774412/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CC=C3N=C2)S1) `REAL300004087680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087680 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CC=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087680 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CC=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087680 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087680 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087680/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087680 Building REAL300004087681 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087681' /scratch/stefan/7774412/working/building/REAL300004087681 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087681 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087681/0 /scratch/stefan/7774412/working/building/REAL300004087681 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/856 `/scratch/stefan/7774412/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)C=NN2C)S1) `REAL300004087681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087681 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)C=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 35, 39, 39, 19, 13, 11, 1, 11, 1, 1, 1, 2, 2, 1, 1, 1, 1, 19, 19, 19, 19, 35, 35, 13, 2, 2, 2, 2, 3, 3, 3, 1, 2, 2, 2] 39 rigid atoms, others: [35, 10, 12, 13, 14, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 173 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087681 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)C=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 19, 19, 21, 21, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 19] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087681 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087681 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087681/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087681 Building REAL300004087682 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087682' /scratch/stefan/7774412/working/building/REAL300004087682 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087682 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087682/0 /scratch/stefan/7774412/working/building/REAL300004087682 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/857 `/scratch/stefan/7774412/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC(=O)C3)N=N2)S1) `REAL300004087682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087682 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC(=O)C3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 11, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 9, 15, 29, 29, 9, 5, 5, 1, 5, 1, 1, 1, 1, 9, 31, 31, 31, 31, 1, 1, 8, 9, 9, 9, 15, 15, 5, 1, 9, 9, 31, 31, 31, 31, 31] 94 rigid atoms, others: [10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087682 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC(=O)C3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 11, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 42, 58, 58, 58, 58, 8, 8, 1, 2, 2, 2, 2, 2, 2, 9, 42, 42, 58, 58, 58, 58, 58] 94 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087682 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CC3CC(=O)C3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 11, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 94, 94, 94, 58, 45, 45, 31, 45, 31, 31, 7, 1, 1, 1, 1, 1, 1, 31, 31, 58, 58, 58, 58, 94, 94, 45, 31, 7, 7, 1, 1, 1, 1, 1] 94 rigid atoms, others: [33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 339 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087682 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087682 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087682/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087682 Building REAL300004087683 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087683' /scratch/stefan/7774412/working/building/REAL300004087683 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087683 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087683/0 /scratch/stefan/7774412/working/building/REAL300004087683 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/858 `/scratch/stefan/7774412/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=NC=CN23)S1) `REAL300004087683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087683 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=NC=CN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 8, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 27, 27, 27, 15, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 27, 27, 13, 1, 1, 1] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 107 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087683 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC3=NC=CN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 8, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087683 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087683 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087683/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087683 Building REAL300004087684 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087684' /scratch/stefan/7774412/working/building/REAL300004087684 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087684 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087684/0 /scratch/stefan/7774412/working/building/REAL300004087684 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/859 `/scratch/stefan/7774412/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3(F)F)C=C2)S1) `REAL300004087684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087684 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 15, 15, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 6, 6, 6, 6, 6, 1, 1] 32 rigid atoms, others: [32, 38, 39, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 73 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: REAL300004087684 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 7, 7, 3, 3, 19, 19, 19, 19, 19, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 19, 19, 19, 19, 19, 7, 7] 32 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087684 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C)CC3(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 32, 32, 32, 19, 15, 13, 1, 13, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 19, 19, 19, 32, 32, 15, 6, 6, 2, 2, 2, 1, 1, 6, 6] 32 rigid atoms, others: [36, 37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 140 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087684 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087684 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087684/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087684 Building REAL300004087685 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087685' /scratch/stefan/7774412/working/building/REAL300004087685 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087685 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087685/0 /scratch/stefan/7774412/working/building/REAL300004087685 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/860 `/scratch/stefan/7774412/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC3=CC=CN=C3C=C2)S1) `REAL300004087685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087685 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC3=CC=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 73, 73, 73, 37, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 73, 73, 21, 6, 6, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087685 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC3=CC=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 2, 2, 3, 9, 9, 37, 37, 37, 37, 37, 37] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087685 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087685 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087685/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087685 Building REAL300004087686 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087686' /scratch/stefan/7774412/working/building/REAL300004087686 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087686 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087686/0 /scratch/stefan/7774412/working/building/REAL300004087686 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/861 `/scratch/stefan/7774412/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C(C)C) `REAL300004087686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087686 none CSC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 19, 18, 24, 24, 24, 13, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19] 39 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087686 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087686/1 /scratch/stefan/7774412/working/building/REAL300004087686 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/862 `/scratch/stefan/7774412/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C(C)C) `REAL300004087686.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087686 none CSC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 102, 66, 13, 66, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 102, 135, 135, 144, 144, 144, 102, 2, 2, 2, 2, 2, 135, 135, 135, 135, 135, 135, 135] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087686 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087686 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087686/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087686/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087686 Building REAL300004087687 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087687' /scratch/stefan/7774412/working/building/REAL300004087687 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087687 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087687/0 /scratch/stefan/7774412/working/building/REAL300004087687 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/863 `/scratch/stefan/7774412/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)NC2=O)S1) `REAL300004087687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087687 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 9, 9, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 1, 9, 9, 9, 9, 9, 9, 9, 1] 21 rigid atoms, others: [38, 10, 12, 13, 14, 15, 16, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 53 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087687 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 16, 16, 16, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 16, 16, 16, 16, 16, 16, 16, 4] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087687 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 21, 21, 21, 16, 16, 16, 9, 16, 9, 9, 9, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 21, 21, 16, 9, 1, 1, 1, 1, 1, 1, 1, 9] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 64 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087687 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087687/1 /scratch/stefan/7774412/working/building/REAL300004087687 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/864 `/scratch/stefan/7774412/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CN=C(C3CCC3)NC2=O)S1) `REAL300004087687.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087687 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CN=C(C3CCC3)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 103, 110, 110, 80, 25, 11, 1, 11, 1, 1, 1, 1, 1, 11, 11, 11, 1, 1, 1, 80, 80, 80, 80, 103, 103, 1, 11, 11, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [37, 10, 12, 13, 14, 15, 16, 20, 21, 22, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 307 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087687 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CN=C(C3CCC3)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 38, 38, 80, 80, 80, 80, 167, 167, 167, 80, 80, 80, 1, 2, 2, 2, 2, 2, 80, 167, 167, 167, 167, 167, 167, 167, 80] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 462 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087687 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CN=C(C3CCC3)NC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 201, 201, 201, 167, 98, 63, 11, 63, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11, 167, 167, 167, 167, 201, 201, 11, 1, 1, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [32, 33, 34, 35, 36, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 509 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087687 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087687 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087687/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087687/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087687 Building REAL300004087688 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087688' /scratch/stefan/7774412/working/building/REAL300004087688 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087688 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087688/0 /scratch/stefan/7774412/working/building/REAL300004087688 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/865 `/scratch/stefan/7774412/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCC3)=NN2C)S1) `REAL300004087688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087688 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 37, 57, 57, 19, 14, 12, 1, 12, 1, 1, 1, 1, 13, 13, 13, 1, 1, 1, 19, 19, 19, 19, 37, 37, 14, 1, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2] 93 rigid atoms, others: [10, 12, 13, 14, 15, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 257 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087688 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 19, 19, 19, 61, 61, 61, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 19, 61, 61, 61, 61, 61, 61, 61, 19, 19, 19] 93 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087688 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CCC3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 8, 8, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 93, 93, 93, 61, 50, 48, 13, 48, 13, 13, 1, 1, 1, 1, 1, 13, 13, 13, 61, 61, 61, 61, 93, 93, 50, 13, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13] 93 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39]) total number of confs: 330 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087688 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087688 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087688/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087688 Building REAL300004087689 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087689' /scratch/stefan/7774412/working/building/REAL300004087689 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087689 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087689/0 /scratch/stefan/7774412/working/building/REAL300004087689 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/866 `/scratch/stefan/7774412/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=NC(C)=C2)S1) `REAL300004087689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087689 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 13, 13, 8, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 6, 1, 2, 2, 2, 2, 2, 2, 1] 13 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087689 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 7, 7, 7, 3, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087689 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087689 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087689/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087689 Building REAL300004087690 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087690' /scratch/stefan/7774412/working/building/REAL300004087690 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087690 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087690/0 /scratch/stefan/7774412/working/building/REAL300004087690 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/867 `/scratch/stefan/7774412/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN=C3C(C)CCCN23)S1) `REAL300004087690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087690 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN=C3C(C)CCCN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 16, 16, 16, 11, 11, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 16, 16, 11, 6, 6, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [32, 33, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087690 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CN=C3C(C)CCCN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 8, 1, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087690 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087690 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087690/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087690 Building REAL300004087691 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087691' /scratch/stefan/7774412/working/building/REAL300004087691 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087691 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087691/0 /scratch/stefan/7774412/working/building/REAL300004087691 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/868 `/scratch/stefan/7774412/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3N=C(C)C=C(C)N3C=C2)S1) `REAL300004087691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087691 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3N=C(C)C=C(C)N3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 5, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 12, 12, 12, 21, 21, 21, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 9, 2, 2, 2, 1, 2, 2, 2, 1, 1] 21 rigid atoms, others: [33, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087691 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3N=C(C)C=C(C)N3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 1, 1, 5, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087691 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087691 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087691/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087691 Building REAL300004087692 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087692' /scratch/stefan/7774412/working/building/REAL300004087692 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087692 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087692/0 /scratch/stefan/7774412/working/building/REAL300004087692 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/869 `/scratch/stefan/7774412/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(F)C=C2)S1) `REAL300004087692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087692 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 69, 69, 69, 40, 29, 25, 4, 25, 1, 4, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 69, 69, 29, 4, 4, 4, 4, 1, 1, 1, 1] 69 rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 273 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087692 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 22, 22, 40, 40, 28, 40, 40, 40, 1, 2, 2, 2, 3, 3, 2, 22, 22, 22, 22, 40, 40, 40, 40] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087692 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087692/1 /scratch/stefan/7774412/working/building/REAL300004087692 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/870 `/scratch/stefan/7774412/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(F)C=C2)S1) `REAL300004087692.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087692/1/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: REAL300004087692 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [149, 149, 149, 149, 201, 201, 201, 149, 58, 15, 4, 15, 1, 4, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 201, 201, 4, 4, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087692 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 12, 59, 59, 118, 118, 149, 149, 123, 149, 149, 149, 1, 2, 2, 2, 2, 2, 118, 118, 118, 118, 149, 149, 149, 149] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087692 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087692 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087692/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087692/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087692 Building REAL300004087693 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087693' /scratch/stefan/7774412/working/building/REAL300004087693 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087693 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087693/0 /scratch/stefan/7774412/working/building/REAL300004087693 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/871 `/scratch/stefan/7774412/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=NC=NN32)S1) `REAL300004087693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087693 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=NC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 17, 17, 17, 14, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 17, 17, 10, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087693 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=NC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 4, 4, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 3, 14, 14, 14, 14, 14, 14, 14, 14] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087693 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087693/1 /scratch/stefan/7774412/working/building/REAL300004087693 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/872 `/scratch/stefan/7774412/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=NC=NN32)S1) `REAL300004087693.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087693/1/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: REAL300004087693 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=NC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 47, 47, 47, 39, 17, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087693 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=NC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 28, 28, 39, 39, 39, 39, 39, 39, 39, 39, 1, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087693 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087693 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087693/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087693/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087693 Building REAL300004087694 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087694' /scratch/stefan/7774412/working/building/REAL300004087694 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087694 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087694/0 /scratch/stefan/7774412/working/building/REAL300004087694 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/873 `/scratch/stefan/7774412/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(O)CCCOC2)S1) `REAL300004087694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087694 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(O)CCCOC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 10, 10, 10, 6, 6, 6, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087694 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(O)CCCOC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 2, 2, 2, 4, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 4, 4, 18, 6, 6, 6, 6, 6, 6, 6, 6] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087694 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087694 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087694/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087694 Building REAL300004087695 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087695' /scratch/stefan/7774412/working/building/REAL300004087695 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087695 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087695/0 /scratch/stefan/7774412/working/building/REAL300004087695 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/874 `/scratch/stefan/7774412/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)OCC(F)(F)F)S1) `REAL300004087695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087695 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)OCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 19, 19, 17, 73, 81, 81, 81, 81, 1, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 81, 81] 115 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 219 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087695 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087695/1 /scratch/stefan/7774412/working/building/REAL300004087695 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/875 `/scratch/stefan/7774412/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)OCC(F)(F)F)S1) `REAL300004087695.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087695 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)OCC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 45, 45, 144, 144, 144, 164, 170, 170, 170, 170, 1, 2, 2, 2, 2, 2, 144, 144, 144, 144, 144, 144, 170, 170] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087695 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087695 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087695/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087695/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087695 Building REAL300004087696 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087696' /scratch/stefan/7774412/working/building/REAL300004087696 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087696 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087696/0 /scratch/stefan/7774412/working/building/REAL300004087696 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/876 `/scratch/stefan/7774412/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C(F)(F)F)S1) `REAL300004087696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087696 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 26, 26, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 10, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087696 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC[C@H]2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087696 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087696 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087696/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087696 Building REAL300004087697 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087697' /scratch/stefan/7774412/working/building/REAL300004087697 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087697 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087697/0 /scratch/stefan/7774412/working/building/REAL300004087697 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/877 `/scratch/stefan/7774412/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C=C3OC2)S1) `REAL300004087697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087697 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C=C3OC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 9, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087697 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C=C3OC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 1, 12, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087697 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087697 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087697/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087697 Building REAL300004087698 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087698' /scratch/stefan/7774412/working/building/REAL300004087698 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087698 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087698/0 /scratch/stefan/7774412/working/building/REAL300004087698 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/878 `/scratch/stefan/7774412/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C1) `REAL300004087698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087698 none CCOC1=CC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [72, 64, 27, 27, 27, 27, 16, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 27, 27, 72, 72, 72, 72, 72, 27, 27, 16, 16, 2, 2, 2, 2, 2, 2, 27] 80 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 206 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087698 none CCOC1=CC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 27, 27, 27, 39, 48, 48, 27, 27, 27, 1, 1, 11, 11, 11, 11, 11, 1, 1, 8, 8, 25, 39, 39, 27, 27, 27, 1] 80 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 38, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087698 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087698/1 /scratch/stefan/7774412/working/building/REAL300004087698 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/879 `/scratch/stefan/7774412/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC=C(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=C1) `REAL300004087698.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087698/1/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: REAL300004087698 none CCOC1=CC=C(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 177, 102, 102, 102, 102, 82, 33, 12, 33, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 102, 102, 179, 179, 179, 179, 179, 102, 102, 82, 82, 3, 3, 2, 2, 2, 102] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087698 none CCOC1=CC=C(CC(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 6, 1, 1, 1, 1, 1, 1, 5, 17, 17, 48, 102, 102, 102, 137, 151, 151, 102, 102, 102, 1, 1, 12, 12, 12, 12, 12, 1, 1, 5, 5, 137, 137, 102, 102, 102, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 21, 22, 28, 29, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087698 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087698 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087698/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087698/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087698 Building REAL300004087699 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087699' /scratch/stefan/7774412/working/building/REAL300004087699 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087699 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087699/0 /scratch/stefan/7774412/working/building/REAL300004087699 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/880 `/scratch/stefan/7774412/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=NC3=CC=CC=C32)S1) `REAL300004087699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087699 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 7, 13, 13, 13, 6, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 13, 13, 4, 2, 2, 2, 1, 1, 1, 1, 1] 13 rigid atoms, others: [33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087699 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=NC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 8, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 7, 7, 7, 6, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 6, 7, 7, 7, 6] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087699 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087699 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087699/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087699 Building REAL300004087700 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087700' /scratch/stefan/7774412/working/building/REAL300004087700 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087700 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087700/0 /scratch/stefan/7774412/working/building/REAL300004087700 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/881 `/scratch/stefan/7774412/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCO1) `REAL300004087700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087700 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [45, 32, 14, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 14, 14, 14, 45, 45, 45, 32, 32, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14] 53 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087700 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 1, 1, 1, 8, 8, 8, 14, 14, 14, 27, 41, 41, 14, 14, 14, 1, 1, 1, 1, 17, 17, 17, 9, 9, 8, 27, 27, 14, 14, 14, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 34, 17, 18, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087700 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087700/1 /scratch/stefan/7774412/working/building/REAL300004087700 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/882 `/scratch/stefan/7774412/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCO1) `REAL300004087700.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087700/1/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: REAL300004087700 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 160, 155, 53, 13, 53, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 155, 155, 155, 155, 178, 178, 178, 160, 160, 2, 2, 2, 2, 2, 155, 155, 155, 155, 155, 155] 201 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087700 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CCCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 1, 1, 1, 13, 13, 53, 155, 155, 155, 201, 201, 201, 155, 155, 155, 1, 1, 1, 1, 8, 8, 8, 4, 4, 201, 201, 155, 155, 155, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 17, 18, 19, 20, 36, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087700 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087700 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087700/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087700/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087700 Building REAL300004087701 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087701' /scratch/stefan/7774412/working/building/REAL300004087701 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087701 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087701/0 /scratch/stefan/7774412/working/building/REAL300004087701 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/883 `/scratch/stefan/7774412/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=CC3=CC=CN=C32)S1) `REAL300004087701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087701 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=CC3=CC=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 15, 15, 15, 11, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 9, 2, 2, 2, 1, 1, 1, 1, 1] 15 rigid atoms, others: [33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087701 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=CC3=CC=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 11, 11, 11, 10, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 10, 11, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087701 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087701 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087701/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087701 Building REAL300004087702 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087702' /scratch/stefan/7774412/working/building/REAL300004087702 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087702 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087702/0 /scratch/stefan/7774412/working/building/REAL300004087702 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/884 `/scratch/stefan/7774412/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)C3(C)C)S1) `REAL300004087702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087702 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 11, 11, 11, 21, 21, 21, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 21 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087702 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 39 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087702 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087702/1 /scratch/stefan/7774412/working/building/REAL300004087702 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/885 `/scratch/stefan/7774412/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)C3(C)C)S1) `REAL300004087702.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087702/1/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: REAL300004087702 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 201, 201, 201, 148, 37, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087702 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 67, 67, 148, 148, 148, 148, 148, 148, 148, 148, 1, 2, 2, 2, 2, 2, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148, 148] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 292 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087702 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087702 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087702/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087702/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087702 Building REAL300004087703 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087703' /scratch/stefan/7774412/working/building/REAL300004087703 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087703 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087703/0 /scratch/stefan/7774412/working/building/REAL300004087703 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/886 `/scratch/stefan/7774412/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C3CC3)C=C2)S1) `REAL300004087703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087703 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 60, 81, 81, 39, 26, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 9, 9, 1, 1, 39, 39, 39, 39, 60, 60, 26, 7, 21, 1, 1, 9, 9, 9, 9, 9, 1, 1] 348 rigid atoms, others: [32, 33, 39, 40, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 343 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087703 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 348 conformations in input total number of sets (complete confs): 348 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 39, 39, 18, 18, 83, 83, 39, 39, 1, 2, 2, 2, 3, 3, 2, 18, 54, 39, 39, 83, 79, 83, 83, 82, 39, 39] 348 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 382 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087703 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 351 conformations in input total number of sets (complete confs): 351 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 117, 117, 117, 82, 61, 61, 27, 61, 9, 27, 9, 10, 10, 1, 1, 1, 1, 10, 10, 82, 82, 82, 82, 117, 117, 61, 27, 81, 10, 10, 1, 1, 1, 1, 1, 10, 10] 351 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 518 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087703 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087703/1 /scratch/stefan/7774412/working/building/REAL300004087703 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/887 `/scratch/stefan/7774412/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C3CC3)C=C2)S1) `REAL300004087703.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087703 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 118, 132, 132, 91, 49, 22, 6, 22, 1, 6, 1, 1, 1, 1, 1, 7, 7, 1, 1, 91, 91, 91, 91, 118, 118, 6, 18, 1, 1, 7, 7, 7, 7, 7, 1, 1] 603 rigid atoms, others: [32, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 417 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087703 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 34, 34, 70, 70, 91, 91, 70, 81, 166, 166, 91, 91, 1, 2, 2, 2, 2, 2, 70, 210, 91, 91, 166, 166, 166, 166, 166, 91, 91] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 880 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087703 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C3CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 98, 50, 19, 50, 7, 19, 7, 7, 7, 1, 1, 1, 1, 7, 7, 166, 166, 166, 166, 201, 201, 19, 57, 7, 7, 1, 1, 1, 1, 1, 7, 7] 603 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39]) total number of confs: 593 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087703 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087703 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087703/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087703/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087703 Building REAL300004087704 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087704' /scratch/stefan/7774412/working/building/REAL300004087704 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087704 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087704/0 /scratch/stefan/7774412/working/building/REAL300004087704 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/888 `/scratch/stefan/7774412/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(F)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(F)=C1) `REAL300004087704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087704 none COC1=CC(F)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087704 none COC1=CC(F)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 15, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 15, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 2, 2, 2, 1, 1, 1, 3, 3, 3, 1, 2, 3, 3, 2, 2, 2, 1] 3 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 33, 20, 21, 22, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 27, 28, 29, 30, 31, 32]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087704 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087704 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087704/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087704 Building REAL300004087705 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087705' /scratch/stefan/7774412/working/building/REAL300004087705 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087705 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087705/0 /scratch/stefan/7774412/working/building/REAL300004087705 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/889 `/scratch/stefan/7774412/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1) `REAL300004087705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087705 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 24, 24, 24, 14, 8, 8, 3, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 14, 14, 14, 14, 24, 24, 8, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 24 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087705 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 2, 2, 13, 14, 14, 13, 14, 14, 14, 13, 14, 14, 14, 14, 14, 1, 2, 2, 2, 3, 3, 2, 13, 14, 14, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087705 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 24, 24, 24, 14, 8, 8, 2, 8, 1, 2, 4, 4, 2, 4, 4, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 24, 24, 8, 2, 4, 4, 2, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [41, 42, 43, 12, 45, 46, 44, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087705 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087705/1 /scratch/stefan/7774412/working/building/REAL300004087705 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/890 `/scratch/stefan/7774412/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1) `REAL300004087705.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087705 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 97, 97, 97, 68, 26, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 68, 68, 68, 68, 97, 97, 2, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 97 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 284 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087705 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 47, 47, 68, 68, 68, 68, 68, 68, 68, 68, 69, 69, 69, 69, 69, 1, 2, 2, 2, 2, 2, 68, 68, 68, 68, 68, 68, 68, 68, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69] 97 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 255 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087705 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C2=CC=CC=C2C)C2CCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 97, 97, 97, 69, 27, 6, 3, 6, 1, 3, 4, 4, 3, 4, 4, 4, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 97, 97, 3, 4, 4, 3, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 97 rigid atoms, others: [40, 41, 42, 43, 12, 45, 46, 44, 48, 49, 50, 20, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 275 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087705 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087705 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087705/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087705/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087705 Building REAL300004087706 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087706' /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087706 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087706/0 /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/891 `/scratch/stefan/7774412/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1) `REAL300004087706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 23, 23, 23, 13, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 13, 13, 13, 13, 23, 23, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 65 rigid atoms, others: [48, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 104 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 38, 38, 38, 38, 38, 38, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 38, 38, 38, 38, 38, 38, 38, 13, 13] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 28] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 154 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 65, 65, 65, 38, 24, 22, 5, 22, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 5, 38, 38, 38, 38, 65, 65, 24, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5] 65 rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49]) total number of confs: 256 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087706/1 /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/892 `/scratch/stefan/7774412/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1) `REAL300004087706.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1] 4 rigid atoms, others: [48, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 2, 2] 4 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 28] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 4, 4] 4 rigid atoms, others: [43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49]) total number of confs: 13 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087706/2 /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/893 `/scratch/stefan/7774412/working/3D/893' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1) `REAL300004087706.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087706/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 20, 20, 19, 8, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1] 26 rigid atoms, others: [48, 34, 35, 36, 37, 38, 39, 47, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 15, 15, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 19, 1, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 19, 19] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 28] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 13, 11, 5, 11, 5, 5, 5, 5, 5, 5, 3, 5, 1, 1, 1, 1, 1, 1, 1, 5, 26, 26, 26, 26, 26, 26, 5, 5, 5, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 5, 5] 26 rigid atoms, others: [42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 57 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087706/3 /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/894 `/scratch/stefan/7774412/working/3D/894' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1) `REAL300004087706.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087706/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 5, 6, 6, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 1, 1] 10 rigid atoms, others: [48, 34, 35, 36, 37, 38, 39, 47, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 7, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 28] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087706 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@]23CC[C@H]2C[N@@H+](CC2=CC=CC=C2)C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 6, 9, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 1, 6, 6] 10 rigid atoms, others: [42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48]) total number of confs: 29 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087706 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087706 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087706/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087706/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087706/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087706/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087706 Building REAL300004087707 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087707' /scratch/stefan/7774412/working/building/REAL300004087707 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087707 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087707/0 /scratch/stefan/7774412/working/building/REAL300004087707 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/895 `/scratch/stefan/7774412/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=NN(C)C=C2)S1) `REAL300004087707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087707 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 129, 129, 129, 80, 60, 60, 13, 60, 1, 13, 13, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 129, 129, 60, 13, 13, 13, 13, 13, 13, 2, 2, 2, 1, 1] 129 rigid atoms, others: [37, 38, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300004087707 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 22, 22, 22, 80, 80, 80, 80, 80, 1, 2, 2, 2, 2, 2, 2, 22, 22, 22, 23, 23, 23, 80, 80, 80, 80, 80] 129 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087707 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087707/1 /scratch/stefan/7774412/working/building/REAL300004087707 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/896 `/scratch/stefan/7774412/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=NN(C)C=C2)S1) `REAL300004087707.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087707/1/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: REAL300004087707 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 175, 175, 175, 169, 109, 71, 12, 71, 1, 12, 12, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 175, 175, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1, 1] 175 rigid atoms, others: [36, 37, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 379 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087707 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=NN(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 23, 23, 91, 91, 91, 169, 169, 169, 169, 169, 1, 2, 2, 2, 2, 2, 91, 91, 91, 91, 91, 91, 169, 169, 169, 169, 169] 175 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 467 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087707 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087707 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087707/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087707/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087707 Building REAL300004087708 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087708' /scratch/stefan/7774412/working/building/REAL300004087708 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087708 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087708/0 /scratch/stefan/7774412/working/building/REAL300004087708 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/897 `/scratch/stefan/7774412/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C(C)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C1) `REAL300004087708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087708 none CC1=CN(C(C)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 22, 3, 22, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 82, 82, 82, 82, 82, 82, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2, 82] 118 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087708 none CC1=CN(C(C)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 63, 63, 67, 82, 82, 82, 118, 118, 118, 82, 82, 82, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 67, 118, 118, 82, 82, 82, 1] 118 rigid atoms, others: [0, 1, 2, 3, 4, 35, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 432 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087708 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087708/1 /scratch/stefan/7774412/working/building/REAL300004087708 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/898 `/scratch/stefan/7774412/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C(C)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=C1) `REAL300004087708.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087708/1/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: REAL300004087708 none CC1=CN(C(C)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 11, 13, 6, 11, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 13] 13 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087708 none CC1=CN(C(C)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 7, 7, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 4, 4, 4, 4, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087708 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087708 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087708/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087708/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087708 Building REAL300004087709 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087709' /scratch/stefan/7774412/working/building/REAL300004087709 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087709 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087709/0 /scratch/stefan/7774412/working/building/REAL300004087709 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/899 `/scratch/stefan/7774412/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1) `REAL300004087709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087709 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 38, 73, 73, 21, 14, 11, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 21, 21, 21, 21, 38, 38, 14, 1, 1, 7, 7, 7, 7, 7] 76 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37]) total number of confs: 276 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: REAL300004087709 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 21, 21, 21, 21, 21, 51, 51, 51, 51, 51, 21, 1, 2, 2, 2, 2, 2, 3, 21, 21, 51, 51, 51, 51, 51] 76 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 122 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087709 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 76, 76, 76, 51, 43, 37, 7, 37, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 51, 51, 51, 51, 76, 76, 43, 7, 7, 1, 1, 1, 1, 1] 76 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 270 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087709 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087709/1 /scratch/stefan/7774412/working/building/REAL300004087709 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/900 `/scratch/stefan/7774412/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1) `REAL300004087709.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087709/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087709 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 109, 163, 192, 192, 109, 27, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 109, 109, 109, 109, 163, 163, 1, 1, 6, 6, 1, 6, 6] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 597 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087709 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 49, 49, 109, 109, 109, 109, 109, 174, 174, 109, 174, 174, 109, 1, 2, 2, 2, 3, 3, 109, 109, 174, 174, 109, 174, 174] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087709 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CSC(C3=CC=CC=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 14, 1, 1, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 174, 201, 201, 201, 174, 78, 28, 6, 28, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 174, 174, 174, 174, 201, 201, 6, 6, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 434 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087709 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087709 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087709/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087709/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087709 Building REAL300004087710 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087710' /scratch/stefan/7774412/working/building/REAL300004087710 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087710 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087710/0 /scratch/stefan/7774412/working/building/REAL300004087710 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/901 `/scratch/stefan/7774412/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(CC)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087710 none CCC1=NN(C)C(CC)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [39, 19, 18, 18, 18, 18, 18, 18, 35, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 39, 39, 39, 39, 38, 19, 19, 19, 35, 35, 35, 35, 35, 2, 2, 2, 2, 2, 2] 107 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 268 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087710 none CCC1=NN(C)C(CC)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 10, 10, 12, 18, 18, 19, 37, 57, 57, 18, 18, 18, 5, 5, 5, 5, 5, 2, 2, 2, 3, 3, 3, 3, 3, 12, 37, 37, 19, 19, 19] 107 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 9, 10] set([0, 8, 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]) total number of confs: 263 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087710 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087710 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087710/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087710 Building REAL300004087711 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087711' /scratch/stefan/7774412/working/building/REAL300004087711 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087711 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087711/0 /scratch/stefan/7774412/working/building/REAL300004087711 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/902 `/scratch/stefan/7774412/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3C=CN=N3)CC2)S1) `REAL300004087711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087711 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3C=CN=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 8, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 50, 76, 76, 27, 15, 13, 1, 13, 1, 1, 13, 13, 13, 13, 1, 1, 27, 27, 27, 27, 50, 50, 15, 13, 13, 1, 1, 1, 1] 126 rigid atoms, others: [32, 10, 12, 13, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 310 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087711 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3C=CN=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 8, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 27, 82, 82, 82, 82, 27, 27, 1, 2, 2, 2, 2, 2, 3, 82, 82, 27, 27, 27, 27] 126 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 168 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087711 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(N3C=CN=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 8, 8, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 126, 126, 126, 82, 63, 60, 13, 60, 1, 1, 1, 1, 1, 1, 13, 13, 82, 82, 82, 82, 126, 126, 63, 1, 1, 13, 13, 13, 13] 126 rigid atoms, others: [12, 13, 14, 15, 16, 17, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32]) total number of confs: 459 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087711 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087711/1 /scratch/stefan/7774412/working/building/REAL300004087711 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/903 `/scratch/stefan/7774412/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3C=CN=N3)CC2)S1) `REAL300004087711.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087711 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3C=CN=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 8, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 15, 15, 14, 9, 7, 1, 7, 1, 1, 9, 9, 9, 9, 1, 1, 14, 14, 14, 14, 14, 14, 9, 9, 1, 1, 1, 1] 18 rigid atoms, others: [10, 12, 13, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087711 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3C=CN=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 8, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 6, 11, 11, 14, 18, 18, 18, 18, 14, 14, 1, 2, 2, 2, 2, 2, 18, 18, 14, 14, 14, 14] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087711 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(N3C=CN=N3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 8, 8, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 14, 13, 9, 13, 1, 1, 1, 1, 1, 1, 9, 9, 18, 18, 18, 18, 18, 18, 1, 1, 9, 9, 9, 9] 18 rigid atoms, others: [12, 13, 14, 15, 16, 17, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 42 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087711 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087711 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087711/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087711/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087711 Building REAL300004087712 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087712' /scratch/stefan/7774412/working/building/REAL300004087712 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087712 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087712/0 /scratch/stefan/7774412/working/building/REAL300004087712 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/904 `/scratch/stefan/7774412/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)CC3)S1) `REAL300004087712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087712 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087712 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCC(CC2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 5, 5, 5, 5, 3, 5, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087712 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087712/1 /scratch/stefan/7774412/working/building/REAL300004087712 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/905 `/scratch/stefan/7774412/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)CC3)S1) `REAL300004087712.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087712/1/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: REAL300004087712 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 161, 161, 161, 111, 21, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 161, 161, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 161 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25]) total number of confs: 437 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087712 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCC(CC2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 59, 59, 112, 112, 59, 112, 112, 112, 112, 1, 2, 2, 2, 2, 2, 112, 112, 112, 112, 59, 112, 112, 112, 112, 112, 112, 112, 112] 161 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087712 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087712 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087712/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087712/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087712 Building REAL300004087713 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087713' /scratch/stefan/7774412/working/building/REAL300004087713 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087713 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087713/0 /scratch/stefan/7774412/working/building/REAL300004087713 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/906 `/scratch/stefan/7774412/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1C1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NO1) `REAL300004087713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087713 none COC1=CC=CC=C1C1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 9, 9, 2, 9, 9, 1, 1, 1, 1, 13, 13, 17, 29, 29, 29, 55, 94, 94, 29, 29, 29, 1, 1, 1, 23, 23, 23, 9, 9, 9, 9, 17, 55, 55, 29, 29, 29, 1] 200 rigid atoms, others: [7, 8, 9, 10, 39, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 418 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087713 none COC1=CC=CC=C1C1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 65, 65, 73, 101, 101, 101, 177, 200, 200, 101, 101, 101, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 73, 177, 177, 101, 101, 101, 9] 200 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087713 none COC1=CC=CC=C1C1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [131, 101, 101, 101, 63, 101, 101, 29, 29, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 29, 29, 29, 131, 131, 131, 101, 101, 101, 101, 2, 2, 2, 2, 2, 2, 29] 200 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 375 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087713 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087713 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087713/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087713 Building REAL300004087714 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087714' /scratch/stefan/7774412/working/building/REAL300004087714 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087714 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087714/0 /scratch/stefan/7774412/working/building/REAL300004087714 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/907 `/scratch/stefan/7774412/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=NN3C=C2)S1) `REAL300004087714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087714 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=NN3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087714 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=NN3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 8, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087714 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087714 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087714/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087714 Building REAL300004087715 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087715' /scratch/stefan/7774412/working/building/REAL300004087715 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087715 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087715/0 /scratch/stefan/7774412/working/building/REAL300004087715 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/908 `/scratch/stefan/7774412/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(CC2=CC=CC=C2)=NO1) `REAL300004087715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087715 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(CC2=CC=CC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 23, 24, 106, 109, 109, 109, 109, 109, 23, 23, 24, 24, 24, 2, 2, 2, 2, 2, 2, 106, 106, 109, 109, 109, 109, 109] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 374 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087715 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(CC2=CC=CC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 13, 24, 24, 24, 47, 63, 63, 23, 23, 23, 1, 1, 7, 12, 12, 9, 12, 12, 1, 1, 2, 2, 2, 13, 47, 47, 24, 24, 24, 7, 7, 12, 12, 11, 12, 12] 201 rigid atoms, others: [0, 1, 2, 3, 16, 17, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 307 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087715 none CC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(CC2=CC=CC=C2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 66, 66, 78, 109, 109, 109, 201, 201, 201, 109, 109, 108, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 13, 13, 78, 201, 201, 109, 109, 109, 4, 4, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 819 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087715 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087715 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087715/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087715 Building REAL300004087716 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087716' /scratch/stefan/7774412/working/building/REAL300004087716 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087716 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087716/0 /scratch/stefan/7774412/working/building/REAL300004087716 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/909 `/scratch/stefan/7774412/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NC2=C1) `REAL300004087716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087716 none COC1=CC(C)=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [30, 23, 23, 23, 23, 23, 23, 23, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 23, 23, 23, 30, 30, 30, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 23, 23] 41 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087716 none COC1=CC(C)=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)NC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 17, 23, 23, 23, 37, 41, 41, 23, 23, 23, 1, 1, 1, 3, 3, 3, 1, 2, 2, 2, 1, 17, 37, 37, 23, 23, 23, 1, 1] 41 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 22, 23, 24, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087716 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087716 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087716/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087716 Building REAL300004087717 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087717' /scratch/stefan/7774412/working/building/REAL300004087717 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087717 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087717/0 /scratch/stefan/7774412/working/building/REAL300004087717 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/910 `/scratch/stefan/7774412/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C(F)=C3N2)S1) `REAL300004087717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087717 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C(F)=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 27, 27, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 26, 26, 10, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087717 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC=C(Cl)C(F)=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'F', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 1, 15, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087717 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087717 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087717/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087717 Building REAL300004087718 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087718' /scratch/stefan/7774412/working/building/REAL300004087718 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087718 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087718/0 /scratch/stefan/7774412/working/building/REAL300004087718 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/911 `/scratch/stefan/7774412/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=NN(C)C3=NC=N2)S1) `REAL300004087718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087718 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=NN(C)C3=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 18, 19, 19, 10, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 18, 18, 9, 1, 2, 2, 2, 1] 19 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087718 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=NN(C)C3=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 8, 5, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 11, 11, 11, 11] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087718 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087718 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087718/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087718 Building REAL300004087719 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087719' /scratch/stefan/7774412/working/building/REAL300004087719 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087719 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087719/0 /scratch/stefan/7774412/working/building/REAL300004087719 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/912 `/scratch/stefan/7774412/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC(C)=C(Cl)C3=NC=C2)S1) `REAL300004087719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087719 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC(C)=C(Cl)C3=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 16, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 19, 19, 9, 1, 1, 2, 2, 2, 1, 1] 19 rigid atoms, others: [32, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 35, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087719 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CC(C)=C(Cl)C3=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 16, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087719 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087719 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087719/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087719 Building REAL300004087720 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087720' /scratch/stefan/7774412/working/building/REAL300004087720 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087720 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087720/0 /scratch/stefan/7774412/working/building/REAL300004087720 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/913 `/scratch/stefan/7774412/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCOC3(CCOCC3)C2)S1) `REAL300004087720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087720 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCOC3(CCOCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 18, 18, 18, 10, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 71 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087720 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCOC3(CCOCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087720 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087720 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087720/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087720 Building REAL300004087721 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087721' /scratch/stefan/7774412/working/building/REAL300004087721 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087721 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087721/0 /scratch/stefan/7774412/working/building/REAL300004087721 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/914 `/scratch/stefan/7774412/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(SC=C3)S2)S1) `REAL300004087721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087721 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(SC=C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 14, 27, 27, 27, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 27, 27, 10, 1, 1, 1] 27 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087721 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(SC=C3)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087721 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087721 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087721/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087721 Building REAL300004087722 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087722' /scratch/stefan/7774412/working/building/REAL300004087722 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087722 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087722/0 /scratch/stefan/7774412/working/building/REAL300004087722 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/915 `/scratch/stefan/7774412/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2Cl)S1) `REAL300004087722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087722 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 7, 7, 7, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 5, 1, 2, 2, 2, 1, 1] 7 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087722 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087722 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087722 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087722/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087722 Building REAL300004087723 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087723' /scratch/stefan/7774412/working/building/REAL300004087723 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087723 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087723/0 /scratch/stefan/7774412/working/building/REAL300004087723 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/916 `/scratch/stefan/7774412/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NN2C(=NN=C2CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087723 none COC1=NN2C(=NN=C2CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 14, 10, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 28, 28, 29, 29, 29, 14, 14, 10, 10, 2, 2, 2, 2, 2, 2, 28, 28] 35 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087723 none COC1=NN2C(=NN=C2CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 8, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16, 22, 22, 26, 28, 28, 28, 34, 35, 35, 28, 28, 28, 1, 1, 2, 2, 2, 7, 7, 16, 16, 26, 34, 34, 29, 29, 29, 1, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 40, 24, 25] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087723 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087723 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087723/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087723 Building REAL300004087724 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087724' /scratch/stefan/7774412/working/building/REAL300004087724 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087724 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087724/0 /scratch/stefan/7774412/working/building/REAL300004087724 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/917 `/scratch/stefan/7774412/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(Cl)C=C3)=NN2C)S1) `REAL300004087724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087724 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(Cl)C=C3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 35, 43, 43, 19, 14, 12, 1, 12, 1, 1, 1, 1, 7, 7, 2, 7, 7, 7, 1, 1, 1, 19, 19, 19, 19, 35, 35, 14, 1, 7, 7, 7, 7, 2, 2, 2] 67 rigid atoms, others: [32, 10, 12, 13, 14, 15, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 197 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087724 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(Cl)C=C3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 19, 19, 19, 39, 39, 36, 39, 39, 39, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 19, 39, 39, 39, 39, 19, 19, 19] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087724 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=C(Cl)C=C3)=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 67, 67, 67, 39, 29, 26, 7, 26, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 39, 39, 39, 39, 67, 67, 29, 7, 1, 1, 1, 1, 7, 7, 7] 67 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 258 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087724 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087724 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087724/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087724 Building REAL300004087725 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087725' /scratch/stefan/7774412/working/building/REAL300004087725 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087725 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087725/0 /scratch/stefan/7774412/working/building/REAL300004087725 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/918 `/scratch/stefan/7774412/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CCOC)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087725 none CCC(CCOC)C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [26, 16, 3, 16, 42, 78, 117, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 32, 32, 32, 32, 32, 16, 45, 45, 78, 76, 117, 117, 117, 2, 2, 2, 2, 2, 2] 198 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 573 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087725 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087725 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087725/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087725 Building REAL300004087726 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087726' /scratch/stefan/7774412/working/building/REAL300004087726 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087726 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087726/0 /scratch/stefan/7774412/working/building/REAL300004087726 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/919 `/scratch/stefan/7774412/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C)=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)OC2=C1) `REAL300004087726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087726 none COC1=CC(C)=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [21, 17, 17, 17, 17, 18, 17, 17, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 17, 17, 21, 21, 21, 17, 18, 18, 18, 17, 2, 2, 2, 2, 2, 2, 17] 35 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087726 none COC1=CC(C)=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)OC2=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 18, 18, 18, 29, 35, 35, 17, 17, 17, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1, 14, 29, 29, 18, 18, 18, 1] 35 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 39, 22, 23, 24, 28] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 29, 30, 31, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087726 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087726 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087726/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087726 Building REAL300004087727 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087727' /scratch/stefan/7774412/working/building/REAL300004087727 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087727 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087727/0 /scratch/stefan/7774412/working/building/REAL300004087727 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/920 `/scratch/stefan/7774412/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CC1=CC=CC=C1) `REAL300004087727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087727 none CCC(CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 3, 8, 13, 25, 25, 25, 25, 25, 25, 42, 48, 48, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 11, 8, 13, 13, 25, 42, 42, 25, 25, 25, 3, 3, 1, 1, 1, 1, 1] 48 rigid atoms, others: [40, 41, 42, 43, 44, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 232 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: REAL300004087727 none CCC(CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [23, 18, 12, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 25, 25, 25, 25, 25, 25, 23, 23, 23, 23, 22, 19, 12, 12, 2, 2, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25, 25] 48 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 172 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087727 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087727 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087727/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087727 Building REAL300004087728 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087728' /scratch/stefan/7774412/working/building/REAL300004087728 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087728 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087728/0 /scratch/stefan/7774412/working/building/REAL300004087728 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/921 `/scratch/stefan/7774412/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=CS1) `REAL300004087728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087728 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 12, 12, 25, 25, 25, 25, 25, 2, 2, 2, 2, 2, 2, 12] 43 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087728 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 8, 8, 10, 12, 12, 12, 23, 24, 24, 12, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 10, 23, 23, 12, 12, 12, 1] 43 rigid atoms, others: [1, 2, 3, 4, 17, 18, 19, 31] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087728 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087728 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087728/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087728 Building REAL300004087729 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087729' /scratch/stefan/7774412/working/building/REAL300004087729 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087729 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087729/0 /scratch/stefan/7774412/working/building/REAL300004087729 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/922 `/scratch/stefan/7774412/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1O) `REAL300004087729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087729 none CC(C)=CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 57, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 5, 11, 83, 83, 83, 83, 83, 83, 83, 57, 57, 13, 2, 2, 2, 2, 2, 2, 13, 13, 26] 282 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 363 number of broken/clashed sets: 214 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087729 none CC(C)=CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 8, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 38, 38, 13, 13, 13, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 8, 8, 1, 9, 25, 25, 13, 13, 13, 1, 1, 2] 282 rigid atoms, others: [34, 4, 5, 6, 7, 8, 41, 42, 21, 22, 23, 24] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 201 number of broken/clashed sets: 214 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087729 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087729 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087729/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087729 Building REAL300004087730 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087730' /scratch/stefan/7774412/working/building/REAL300004087730 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087730 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087730/0 /scratch/stefan/7774412/working/building/REAL300004087730 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/923 `/scratch/stefan/7774412/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C)C3=CC=CC=C32)S1) `REAL300004087730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087730 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 27, 27, 27, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 27, 27, 10, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 27 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087730 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087730 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087730 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087730/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087730 Building REAL300004087731 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087731' /scratch/stefan/7774412/working/building/REAL300004087731 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087731 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087731/0 /scratch/stefan/7774412/working/building/REAL300004087731 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/924 `/scratch/stefan/7774412/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3SC=CN23)S1) `REAL300004087731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087731 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3SC=CN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 26, 26, 26, 16, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 26, 26, 11, 1, 1, 1] 26 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087731 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3SC=CN23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087731 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087731 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087731/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087731 Building REAL300004087732 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087732' /scratch/stefan/7774412/working/building/REAL300004087732 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087732 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087732/0 /scratch/stefan/7774412/working/building/REAL300004087732 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/925 `/scratch/stefan/7774412/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1) `REAL300004087732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087732 none CC1=NC=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 10, 6, 2, 2, 2, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 20, 21, 21, 21, 20, 10, 10, 6, 6, 2, 3, 3, 2, 2, 2] 39 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 88 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087732 none CC1=NC=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 10, 18, 18, 20, 20, 20, 21, 39, 39, 39, 20, 21, 20, 1, 2, 2, 2, 1, 8, 8, 10, 10, 20, 39, 39, 21, 21, 21] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087732 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087732 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087732/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087732 Building REAL300004087733 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087733' /scratch/stefan/7774412/working/building/REAL300004087733 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087733 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087733/0 /scratch/stefan/7774412/working/building/REAL300004087733 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/926 `/scratch/stefan/7774412/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC(C3CC3)=N2)S1) `REAL300004087733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087733 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC(C3CC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 11, 11, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 8, 3, 3, 3, 3, 5, 5, 3, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 24] 26 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 91 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087733 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC(C3CC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 26, 26, 11, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 11, 11, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087733 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC(C3CC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 24, 26, 24, 24, 24, 24, 24, 10, 10, 10, 10, 1, 1, 1, 1, 10, 26, 26, 26, 26, 26, 26, 26, 24, 24, 24, 24, 10, 10, 1, 1, 1, 1, 1] 26 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 38 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087733 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2N2C=CC(C3CC3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 15, 19, 19, 11, 11, 11, 8, 11, 8, 8, 7, 8, 8, 1, 1, 1, 1, 1, 1, 10, 10, 1, 11, 11, 11, 11, 15, 15, 11, 8, 8, 8, 8, 1, 1, 10, 10, 10, 10, 10] 26 rigid atoms, others: [37, 38, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087733 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087733 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087733/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087733 Building REAL300004087734 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087734' /scratch/stefan/7774412/working/building/REAL300004087734 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087734 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087734/0 /scratch/stefan/7774412/working/building/REAL300004087734 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/927 `/scratch/stefan/7774412/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3=CC=CC=C3C2)S1) `REAL300004087734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087734 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3=CC=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 18, 18, 18, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 18, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 75 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087734 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CC3=CC=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087734 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087734/1 /scratch/stefan/7774412/working/building/REAL300004087734 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/928 `/scratch/stefan/7774412/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3=CC=CC=C3C2)S1) `REAL300004087734.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087734/1/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: REAL300004087734 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3=CC=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 201, 201, 201, 152, 43, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087734 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CC3=CC=CC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 55, 55, 152, 152, 152, 152, 152, 152, 152, 152, 151, 1, 2, 2, 2, 2, 2, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152, 152] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087734 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087734 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087734/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087734/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087734 Building REAL300004087735 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087735' /scratch/stefan/7774412/working/building/REAL300004087735 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087735 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087735/0 /scratch/stefan/7774412/working/building/REAL300004087735 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/929 `/scratch/stefan/7774412/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(F)C(Cl)=C2)S1) `REAL300004087735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087735 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(F)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 119, 119, 119, 68, 55, 49, 12, 49, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 68, 69, 69, 69, 119, 119, 55, 12, 13, 13, 13, 1, 1, 1] 119 rigid atoms, others: [33, 34, 35, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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: REAL300004087735 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC=C(F)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 21, 21, 68, 68, 60, 68, 68, 68, 68, 1, 2, 2, 2, 3, 3, 2, 21, 22, 22, 22, 68, 68, 68] 119 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087735 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087735/1 /scratch/stefan/7774412/working/building/REAL300004087735 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/930 `/scratch/stefan/7774412/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(F)C(Cl)=C2)S1) `REAL300004087735.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087735/1/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: REAL300004087735 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(F)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [158, 158, 158, 158, 201, 201, 201, 158, 72, 28, 10, 28, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 201, 201, 10, 10, 10, 10, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 526 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087735 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC=C(F)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 12, 36, 36, 82, 82, 158, 158, 142, 158, 158, 158, 158, 1, 2, 2, 2, 2, 2, 82, 82, 82, 82, 158, 158, 158] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087735 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087735 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087735/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087735/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087735 Building REAL300004087736 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087736' /scratch/stefan/7774412/working/building/REAL300004087736 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087736 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087736/0 /scratch/stefan/7774412/working/building/REAL300004087736 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/931 `/scratch/stefan/7774412/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=CC3=C(C)C=CC=C23)S1) `REAL300004087736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087736 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=CC3=C(C)C=CC=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 21, 21, 21, 11, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 9, 1, 1, 2, 2, 2, 1, 1, 1] 21 rigid atoms, others: [35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 93 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087736 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC=CC3=C(C)C=CC=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 1, 1, 1, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087736 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087736 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087736/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087736 Building REAL300004087737 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087737' /scratch/stefan/7774412/working/building/REAL300004087737 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087737 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087737/0 /scratch/stefan/7774412/working/building/REAL300004087737 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/932 `/scratch/stefan/7774412/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087737 none CCCN1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [52, 46, 14, 14, 14, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 52, 52, 52, 52, 52, 46, 46, 14, 14, 2, 2, 2, 2, 2, 2] 85 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087737 none CCCN1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [17, 9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 14, 14, 14, 25, 41, 41, 14, 14, 14, 1, 17, 17, 17, 17, 17, 9, 9, 1, 1, 11, 25, 25, 14, 14, 14] 85 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087737 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087737 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087737/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087737 Building REAL300004087738 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087738' /scratch/stefan/7774412/working/building/REAL300004087738 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087738 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087738/0 /scratch/stefan/7774412/working/building/REAL300004087738 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/933 `/scratch/stefan/7774412/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(F)C(OC(F)(F)F)=C2)S1) `REAL300004087738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087738 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(F)C(OC(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 41, 41, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1] 123 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087738 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(F)C(OC(F)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 15, 1, 12, 5, 15, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 65, 65, 65, 65, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13] 123 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087738 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087738 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087738/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087738 Building REAL300004087739 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087739' /scratch/stefan/7774412/working/building/REAL300004087739 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087739 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087739/0 /scratch/stefan/7774412/working/building/REAL300004087739 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/934 `/scratch/stefan/7774412/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087739 none CCC(C)N1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [55, 45, 22, 45, 22, 22, 22, 22, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 56, 56, 56, 56, 56, 45, 45, 45, 45, 22, 22, 2, 2, 2, 2, 2, 2] 86 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 242 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087739 none CCC(C)N1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 1, 6, 1, 1, 1, 1, 1, 1, 10, 10, 14, 22, 22, 22, 39, 65, 65, 22, 22, 22, 10, 10, 10, 10, 10, 6, 6, 6, 6, 1, 1, 14, 39, 39, 22, 22, 22] 86 rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087739 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087739 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087739/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087739 Building REAL300004087740 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087740' /scratch/stefan/7774412/working/building/REAL300004087740 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087740 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087740/0 /scratch/stefan/7774412/working/building/REAL300004087740 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/935 `/scratch/stefan/7774412/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC3=CC=C(F)C=C32)S1) `REAL300004087740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087740 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC3=CC=C(F)C=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087740 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC3=CC=C(F)C=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087740 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087740 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087740/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087740 Building REAL300004087741 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087741' /scratch/stefan/7774412/working/building/REAL300004087741 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087741 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087741/0 /scratch/stefan/7774412/working/building/REAL300004087741 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/936 `/scratch/stefan/7774412/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(Br)C=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087741 none COC1=C(Br)C=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 12, 12, 12, 12, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 18, 18, 18, 12, 12, 12, 2, 2, 2, 2, 2, 2] 30 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087741 none COC1=C(Br)C=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 12, 12, 12, 22, 26, 26, 12, 12, 12, 2, 2, 2, 1, 1, 1, 10, 22, 22, 12, 12, 12] 30 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087741 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087741 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087741/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087741 Building REAL300004087742 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087742' /scratch/stefan/7774412/working/building/REAL300004087742 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087742 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087742/0 /scratch/stefan/7774412/working/building/REAL300004087742 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/937 `/scratch/stefan/7774412/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)CC(F)(F)F)S1) `REAL300004087742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087742 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H](C)CC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 19, 19] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087742 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087742 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087742/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087742 Building REAL300004087743 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087743' /scratch/stefan/7774412/working/building/REAL300004087743 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087743 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087743/0 /scratch/stefan/7774412/working/building/REAL300004087743 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/938 `/scratch/stefan/7774412/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(O)C(C)=C2C)S1) `REAL300004087743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087743 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(O)C(C)=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 1, 1, 2, 2, 2, 2, 2, 2, 2] 18 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087743 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(O)C(C)=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.3', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 5, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 10, 5, 5, 5, 5, 5, 5] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087743 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087743 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087743/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087743 Building REAL300004087744 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087744' /scratch/stefan/7774412/working/building/REAL300004087744 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087744 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087744/0 /scratch/stefan/7774412/working/building/REAL300004087744 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/939 `/scratch/stefan/7774412/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CSC[C@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087744 none CCC(=O)N1CSC[C@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 9, 11, 9, 9, 9, 9, 2, 9, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 18, 18, 18, 18, 18, 9, 9, 9, 9, 2, 2, 2, 2, 2, 2] 30 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087744 none CCC(=O)N1CSC[C@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 15, 24, 24, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 5, 15, 15, 9, 9, 9] 30 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087744 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087744/1 /scratch/stefan/7774412/working/building/REAL300004087744 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/940 `/scratch/stefan/7774412/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N1CSC[C@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087744.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087744/1/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: REAL300004087744 none CCC(=O)N1CSC[C@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [117, 91, 77, 91, 77, 77, 77, 77, 56, 77, 12, 56, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 117, 117, 117, 117, 117, 77, 77, 77, 77, 2, 2, 1, 1, 1] 145 rigid atoms, others: [34, 35, 36, 12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 435 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087744 none CCC(=O)N1CSC[C@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 77, 77, 77, 124, 138, 138, 77, 77, 77, 11, 11, 11, 11, 11, 1, 1, 1, 1, 124, 124, 77, 77, 77] 145 rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36]) total number of confs: 474 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087744 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087744 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087744/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087744/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087744 Building REAL300004087745 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087745' /scratch/stefan/7774412/working/building/REAL300004087745 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087745 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087745/0 /scratch/stefan/7774412/working/building/REAL300004087745 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/941 `/scratch/stefan/7774412/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3[C@H](C2)C3(F)F)S1) `REAL300004087745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087745 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3[C@H](C2)C3(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 29, 29, 29, 17, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 29, 29, 13, 1, 1, 1, 1] 29 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 115 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087745 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3[C@H](C2)C3(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 69 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087745 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087745 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087745/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087745 Building REAL300004087746 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087746' /scratch/stefan/7774412/working/building/REAL300004087746 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087746 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087746/0 /scratch/stefan/7774412/working/building/REAL300004087746 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/942 `/scratch/stefan/7774412/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC(C)C)=C2Cl)S1) `REAL300004087746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087746 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC(C)C)=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 7, 7, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 9, 9, 1, 1, 3, 3, 3, 3, 5, 5, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9] 15 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 41 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087746 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OC(C)C)=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 13, 13, 13, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 41 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087746 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087746 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087746/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087746 Building REAL300004087747 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087747' /scratch/stefan/7774412/working/building/REAL300004087747 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087747 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087747/0 /scratch/stefan/7774412/working/building/REAL300004087747 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/943 `/scratch/stefan/7774412/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=C(C4=CC=CC=C4)NC3=C2)S1) `REAL300004087747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087747 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=C(C4=CC=CC=C4)NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 27, 27, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1] 49 rigid atoms, others: [34, 35, 36, 10, 43, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087747 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=C(C4=CC=CC=C4)NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 35, 35, 13, 35, 35, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 35, 35, 21, 35, 35, 13, 13] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087747 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=C(C4=CC=CC=C4)NC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 49, 49, 49, 35, 27, 22, 5, 22, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 35, 35, 35, 35, 49, 49, 27, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5] 49 rigid atoms, others: [37, 38, 39, 40, 41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43]) total number of confs: 168 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087747 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087747 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087747/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087747 Building REAL300004087748 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087748' /scratch/stefan/7774412/working/building/REAL300004087748 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087748 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087748/0 /scratch/stefan/7774412/working/building/REAL300004087748 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/944 `/scratch/stefan/7774412/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1) `REAL300004087748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087748 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 21, 21, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9] 39 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087748 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 13, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 13, 13, 24, 24, 24, 24] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087748 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 39, 39, 39, 24, 19, 19, 9, 19, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 39, 39, 19, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1] 39 rigid atoms, others: [44, 45, 46, 47, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 153 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087748 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087748/1 /scratch/stefan/7774412/working/building/REAL300004087748 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/945 `/scratch/stefan/7774412/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1) `REAL300004087748.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087748 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 90, 115, 115, 58, 15, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 10, 58, 58, 58, 58, 90, 90, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 387 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087748 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 40, 40, 58, 58, 58, 58, 58, 58, 77, 155, 155, 155, 155, 155, 155, 1, 2, 2, 2, 2, 2, 58, 58, 58, 58, 58, 58, 58, 58, 58, 77, 77, 155, 155, 155, 155] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087748 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCCN2CC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 155, 155, 155, 201, 201, 201, 155, 61, 21, 10, 21, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 201, 201, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 46, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 519 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087748 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087748 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087748/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087748/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087748 Building REAL300004087749 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087749' /scratch/stefan/7774412/working/building/REAL300004087749 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087749 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087749/0 /scratch/stefan/7774412/working/building/REAL300004087749 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/946 `/scratch/stefan/7774412/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCCC3)O2)S1) `REAL300004087749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087749 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 12, 12, 12, 21, 21, 21, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087749 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(CCCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087749 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087749 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087749/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087749 Building REAL300004087750 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087750' /scratch/stefan/7774412/working/building/REAL300004087750 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087750 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087750/0 /scratch/stefan/7774412/working/building/REAL300004087750 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/947 `/scratch/stefan/7774412/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CNN=C3)C=C2)S1) `REAL300004087750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087750 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CNN=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 3, 3, 3, 1, 1] 13 rigid atoms, others: [35, 36, 10, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087750 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CNN=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 13, 13, 13, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087750 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CNN=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 5, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 1, 1, 5, 5] 13 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087750 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087750 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087750/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087750 Building REAL300004087751 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087751' /scratch/stefan/7774412/working/building/REAL300004087751 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087751 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087751/0 /scratch/stefan/7774412/working/building/REAL300004087751 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/948 `/scratch/stefan/7774412/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(F)C=C2C)S1) `REAL300004087751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087751 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(F)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 23, 39, 39, 39, 23, 19, 17, 6, 17, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 39, 39, 19, 6, 18, 1, 1, 1, 2, 2, 2] 117 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 183 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087751 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(F)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 19, 20, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 2, 2, 2, 20, 60, 23, 23, 23, 23, 23, 23] 117 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087751 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087751/1 /scratch/stefan/7774412/working/building/REAL300004087751 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/949 `/scratch/stefan/7774412/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(F)C=C2C)S1) `REAL300004087751.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087751/1/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: REAL300004087751 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(F)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 201, 201, 201, 160, 69, 26, 8, 26, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 201, 201, 8, 24, 1, 1, 1, 2, 2, 2] 603 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 548 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087751 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(F)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 15, 1, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 46, 46, 117, 117, 160, 160, 137, 137, 160, 160, 160, 1, 2, 2, 2, 3, 3, 117, 351, 160, 160, 160, 160, 160, 160] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 933 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087751 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087751 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087751/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087751/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087751 Building REAL300004087752 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087752' /scratch/stefan/7774412/working/building/REAL300004087752 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087752 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087752/0 /scratch/stefan/7774412/working/building/REAL300004087752 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/950 `/scratch/stefan/7774412/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=NOC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087752 none COCC1=NOC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [37, 31, 15, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 37, 37, 37, 31, 31, 2, 2, 2, 2, 2, 2, 15] 57 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087752 none COCC1=NOC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [19, 7, 1, 1, 1, 1, 1, 1, 9, 9, 11, 15, 15, 15, 25, 33, 33, 15, 14, 14, 1, 20, 20, 20, 7, 7, 11, 25, 25, 15, 15, 15, 1] 57 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 20] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087752 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087752 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087752/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087752 Building REAL300004087753 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087753' /scratch/stefan/7774412/working/building/REAL300004087753 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087753 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087753/0 /scratch/stefan/7774412/working/building/REAL300004087753 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/951 `/scratch/stefan/7774412/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C#N)CC23CCOCC3)S1) `REAL300004087753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087753 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C#N)CC23CCOCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [9, 10, 10, 10, 18, 18, 18, 10, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087753 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C#N)CC23CCOCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 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 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087753 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087753/1 /scratch/stefan/7774412/working/building/REAL300004087753 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/952 `/scratch/stefan/7774412/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C#N)CC23CCOCC3)S1) `REAL300004087753.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087753/1/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: REAL300004087753 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C#N)CC23CCOCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 75, 103, 103, 103, 75, 24, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087753 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C#N)CC23CCOCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 63, 63, 75, 75, 75, 75, 75, 75, 75, 75, 75, 1, 2, 2, 2, 2, 2, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75] 103 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087753 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087753 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087753/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087753/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087753 Building REAL300004087754 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087754' /scratch/stefan/7774412/working/building/REAL300004087754 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087754 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087754/0 /scratch/stefan/7774412/working/building/REAL300004087754 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/953 `/scratch/stefan/7774412/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1) `REAL300004087754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087754 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 37, 53, 53, 19, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 19, 19, 19, 19, 37, 37, 13, 1, 1, 1, 1, 9, 9, 9, 9] 82 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 220 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087754 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 19, 19, 19, 19, 19, 19, 19, 62, 62, 62, 62, 62, 1, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 62, 62, 62, 62] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 133 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087754 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 82, 82, 82, 62, 52, 45, 9, 45, 9, 9, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 82, 82, 52, 9, 9, 9, 9, 1, 1, 1, 1] 82 rigid atoms, others: [36, 37, 38, 39, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 271 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087754 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087754/1 /scratch/stefan/7774412/working/building/REAL300004087754 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/954 `/scratch/stefan/7774412/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1) `REAL300004087754.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087754 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 147, 160, 160, 107, 33, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 107, 107, 107, 107, 147, 147, 1, 1, 1, 1, 8, 8, 8, 8] 201 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087754 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 55, 55, 107, 107, 107, 107, 107, 107, 107, 171, 171, 171, 171, 171, 1, 2, 2, 2, 2, 2, 107, 107, 107, 107, 171, 171, 171, 171] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087754 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 201, 201, 201, 171, 85, 33, 8, 33, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 201, 201, 8, 8, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 459 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087754 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087754 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087754/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087754/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087754 Building REAL300004087755 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087755' /scratch/stefan/7774412/working/building/REAL300004087755 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087755 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087755/0 /scratch/stefan/7774412/working/building/REAL300004087755 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/955 `/scratch/stefan/7774412/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C2C=C1) `REAL300004087755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087755 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 8, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 12, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8] 17 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087755 none COC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C2=NC=CC=C2C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 1, 1, 7, 7, 8, 8, 8, 8, 15, 17, 17, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 15, 15, 8, 8, 8, 1, 1, 1, 1, 1] 17 rigid atoms, others: [1, 2, 3, 4, 37, 35, 34, 17, 18, 19, 20, 21, 22, 23, 24, 36, 38] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087755 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087755 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087755/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087755 Building REAL300004087756 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087756' /scratch/stefan/7774412/working/building/REAL300004087756 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087756 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087756/0 /scratch/stefan/7774412/working/building/REAL300004087756 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/956 `/scratch/stefan/7774412/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C#N)CC23CCC3)S1) `REAL300004087756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087756 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C#N)CC23CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 12, 12, 12, 22, 22, 22, 12, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087756 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C#N)CC23CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087756 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087756/1 /scratch/stefan/7774412/working/building/REAL300004087756 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/957 `/scratch/stefan/7774412/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C#N)CC23CCC3)S1) `REAL300004087756.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087756/1/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: REAL300004087756 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C#N)CC23CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [151, 151, 151, 151, 201, 201, 201, 151, 39, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25]) 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: REAL300004087756 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C#N)CC23CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.1', 'N.1', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 8, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 83, 83, 151, 151, 151, 151, 151, 151, 151, 1, 2, 2, 2, 2, 2, 151, 151, 151, 151, 151, 151, 151, 151] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087756 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087756 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087756/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087756/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087756 Building REAL300004087757 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087757' /scratch/stefan/7774412/working/building/REAL300004087757 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087757 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087757/0 /scratch/stefan/7774412/working/building/REAL300004087757 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/958 `/scratch/stefan/7774412/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(F)(F)F)CC3(CCC3)C2)S1) `REAL300004087757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087757 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(F)(F)F)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 19, 19, 19, 10, 6, 6, 1, 6, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 81 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087757 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(F)(F)F)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 47 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087757 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087757/1 /scratch/stefan/7774412/working/building/REAL300004087757 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/959 `/scratch/stefan/7774412/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(F)(F)F)CC3(CCC3)C2)S1) `REAL300004087757.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087757/1/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: REAL300004087757 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(F)(F)F)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 29, 6, 1, 6, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 23, 24, 25, 26, 27, 28]) total number of confs: 519 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087757 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(F)(F)F)CC3(CCC3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 71, 71, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 1, 2, 2, 2, 3, 3, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 422 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087757 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087757 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087757/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087757/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087757 Building REAL300004087758 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087758' /scratch/stefan/7774412/working/building/REAL300004087758 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087758 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087758/0 /scratch/stefan/7774412/working/building/REAL300004087758 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/960 `/scratch/stefan/7774412/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(F)(F)C2=CC=CN=C2)S1) `REAL300004087758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087758 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(F)(F)C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 201, 201, 201, 162, 96, 46, 11, 46, 1, 11, 11, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087758 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(F)(F)C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 59, 59, 135, 135, 133, 162, 162, 162, 162, 162, 1, 2, 2, 2, 2, 2, 162, 162, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 549 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087758 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087758/1 /scratch/stefan/7774412/working/building/REAL300004087758 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/961 `/scratch/stefan/7774412/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(F)(F)C2=CC=CN=C2)S1) `REAL300004087758.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087758/1/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: REAL300004087758 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(F)(F)C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 111, 159, 159, 159, 111, 69, 67, 12, 67, 1, 12, 12, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 159, 159, 69, 1, 1, 1, 1] 159 rigid atoms, others: [12, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087758 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(F)(F)C2=CC=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 15, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 26, 26, 26, 111, 111, 111, 111, 111, 1, 2, 2, 2, 3, 3, 2, 111, 111, 111, 111] 159 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087758 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087758 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087758/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087758/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087758 Building REAL300004087759 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087759' /scratch/stefan/7774412/working/building/REAL300004087759 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087759 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087759/0 /scratch/stefan/7774412/working/building/REAL300004087759 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/962 `/scratch/stefan/7774412/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CCOC3)S1) `REAL300004087759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087759 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CCOC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 15, 15, 15, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087759 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CCOC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 3, 3, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087759 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087759 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087759/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087759 Building REAL300004087760 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087760' /scratch/stefan/7774412/working/building/REAL300004087760 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087760 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087760/0 /scratch/stefan/7774412/working/building/REAL300004087760 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/963 `/scratch/stefan/7774412/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCOCC1) `REAL300004087760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087760 none COCC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 25, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 25, 25, 25, 25, 25, 34, 34, 34, 34, 34, 14, 14, 2, 2, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25, 25, 25] 59 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 150 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087760 none COCC1(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 1, 1, 1, 7, 21, 21, 21, 25, 25, 25, 45, 47, 47, 25, 25, 25, 1, 1, 1, 1, 1, 14, 14, 14, 10, 10, 7, 7, 21, 45, 45, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 236 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087760 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087760 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087760/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087760 Building REAL300004087761 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087761' /scratch/stefan/7774412/working/building/REAL300004087761 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087761 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087761/0 /scratch/stefan/7774412/working/building/REAL300004087761 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/964 `/scratch/stefan/7774412/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1) `REAL300004087761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087761 none CCC(O)(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 1, 7, 7, 24, 24, 24, 33, 33, 33, 53, 65, 65, 33, 33, 33, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 21, 24, 53, 53, 33, 33, 33, 1, 1, 1, 1, 1] 195 rigid atoms, others: [2, 35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087761 none CCC(O)(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 2, 17, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 33, 33, 18, 33, 33, 27, 27, 27, 27, 27, 51, 2, 2, 2, 2, 2, 2, 33, 33, 25, 33, 33] 195 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087761 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087761/1 /scratch/stefan/7774412/working/building/REAL300004087761 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/965 `/scratch/stefan/7774412/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1) `REAL300004087761.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087761/1/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: REAL300004087761 none CCC(O)(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 1, 5, 5, 23, 23, 70, 152, 152, 152, 184, 201, 201, 152, 152, 152, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 15, 184, 184, 152, 152, 152, 1, 1, 1, 1, 1] 603 rigid atoms, others: [34, 35, 36, 37, 38, 2, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 529 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087761 none CCC(O)(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [159, 142, 51, 142, 13, 51, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 142, 152, 152, 142, 152, 152, 159, 159, 159, 159, 159, 426, 2, 2, 2, 2, 2, 152, 152, 143, 152, 152] 603 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1086 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087761 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087761 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087761/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087761/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087761 Building REAL300004087762 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087762' /scratch/stefan/7774412/working/building/REAL300004087762 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087762 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087762/0 /scratch/stefan/7774412/working/building/REAL300004087762 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/966 `/scratch/stefan/7774412/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCCC3=N2)S1) `REAL300004087762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087762 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCCC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 16, 16, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 9, 9, 9, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087762 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCCC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087762 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087762 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087762/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087762 Building REAL300004087763 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087763' /scratch/stefan/7774412/working/building/REAL300004087763 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087763 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087763/0 /scratch/stefan/7774412/working/building/REAL300004087763 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/967 `/scratch/stefan/7774412/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3=CC=CC=N3)C=C2)S1) `REAL300004087763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087763 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3=CC=CC=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 13, 25, 25, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 9, 33, 33, 33, 33, 33, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 33, 33, 33, 33, 1, 1] 187 rigid atoms, others: [32, 33, 38, 39, 10, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 134 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087763 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3=CC=CC=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 47, 97, 97, 97, 97, 97, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 97, 97, 97, 97, 7, 7] 187 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087763 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(OC3=CC=CC=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 187, 187, 187, 97, 69, 65, 28, 65, 8, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 33, 33, 97, 97, 97, 97, 187, 187, 69, 33, 33, 1, 1, 1, 1, 33, 33] 187 rigid atoms, others: [34, 35, 36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 833 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087763 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087763 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087763/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087763 Building REAL300004087764 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087764' /scratch/stefan/7774412/working/building/REAL300004087764 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087764 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087764/0 /scratch/stefan/7774412/working/building/REAL300004087764 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/968 `/scratch/stefan/7774412/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2CCCC3)S1) `REAL300004087764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087764 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 32, 33, 33, 18, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 32, 32, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 133 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087764 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2CCCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087764 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087764 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087764/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087764 Building REAL300004087765 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087765' /scratch/stefan/7774412/working/building/REAL300004087765 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087765 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087765/0 /scratch/stefan/7774412/working/building/REAL300004087765 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/969 `/scratch/stefan/7774412/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(C)(C)C)=NO2)S1) `REAL300004087765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087765 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(C)(C)C)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 15, 26, 30, 30, 15, 10, 8, 1, 8, 1, 1, 1, 1, 4, 4, 4, 1, 1, 14, 15, 15, 15, 26, 26, 11, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 44 rigid atoms, others: [10, 12, 13, 14, 15, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37]) 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: REAL300004087765 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(C)(C)C)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 26, 26, 26, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26] 44 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087765 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087765 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087765/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087765 Building REAL300004087766 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087766' /scratch/stefan/7774412/working/building/REAL300004087766 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087766 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087766/0 /scratch/stefan/7774412/working/building/REAL300004087766 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/970 `/scratch/stefan/7774412/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC)CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1) `REAL300004087766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087766 none CCC1(CC)CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [23, 13, 13, 13, 25, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 23, 23, 23, 23, 23, 25, 25, 25, 25, 25, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13] 45 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 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: 190 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087766 none CCC1(CC)CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 4, 1, 1, 1, 9, 9, 9, 13, 13, 13, 24, 28, 28, 13, 13, 13, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 1, 1, 1, 9, 24, 24, 13, 13, 13, 1, 1] 45 rigid atoms, others: [32, 1, 2, 3, 5, 6, 7, 40, 41, 20, 33, 31] set([0, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087766 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087766 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087766/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087766 Building REAL300004087767 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087767' /scratch/stefan/7774412/working/building/REAL300004087767 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087767 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087767/0 /scratch/stefan/7774412/working/building/REAL300004087767 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/971 `/scratch/stefan/7774412/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C2Cl)OCO3)S1) `REAL300004087767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087767 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C2Cl)OCO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 12, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 1, 1, 1, 1] 5 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087767 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C2Cl)OCO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 12, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087767 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087767 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087767/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087767 Building REAL300004087768 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087768' /scratch/stefan/7774412/working/building/REAL300004087768 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087768 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087768/0 /scratch/stefan/7774412/working/building/REAL300004087768 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/972 `/scratch/stefan/7774412/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC3=C(C(F)(F)F)C=CC=C23)S1) `REAL300004087768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087768 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC3=C(C(F)(F)F)C=CC=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 1, 1, 1, 1, 1] 13 rigid atoms, others: [33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 19, 20, 21, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087768 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=CC3=C(C(F)(F)F)C=CC=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087768 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087768 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087768/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087768 Building REAL300004087769 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087769' /scratch/stefan/7774412/working/building/REAL300004087769 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087769 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087769/0 /scratch/stefan/7774412/working/building/REAL300004087769 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/973 `/scratch/stefan/7774412/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)N3CCCCC3=N2)S1) `REAL300004087769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087769 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)N3CCCCC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 33, 33, 33, 19, 12, 10, 1, 10, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 12, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [45, 38, 39, 40, 41, 10, 43, 12, 13, 14, 44, 17, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 136 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087769 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)N3CCCCC3=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 8, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 19, 20, 20, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087769 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087769 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087769/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087769 Building REAL300004087770 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087770' /scratch/stefan/7774412/working/building/REAL300004087770 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087770 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087770/0 /scratch/stefan/7774412/working/building/REAL300004087770 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/974 `/scratch/stefan/7774412/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=NC3=NC=NN32)S1) `REAL300004087770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087770 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=NC3=NC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 8, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 6, 7, 7, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 6, 6, 3, 1, 2, 2, 2, 1] 7 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087770 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C)=NC3=NC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 8, 1, 8, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 5, 5, 5, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087770 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087770 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087770/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087770 Building REAL300004087771 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087771' /scratch/stefan/7774412/working/building/REAL300004087771 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087771 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087771/0 /scratch/stefan/7774412/working/building/REAL300004087771 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/975 `/scratch/stefan/7774412/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3[C@H](C2)C3(C)C)S1) `REAL300004087771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087771 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3[C@H](C2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 33, 33, 33, 19, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 33, 33, 13, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 33 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087771 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@@H]3[C@H](C2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 7, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087771 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087771 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087771/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087771 Building REAL300004087772 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087772' /scratch/stefan/7774412/working/building/REAL300004087772 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087772 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087772/0 /scratch/stefan/7774412/working/building/REAL300004087772 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/976 `/scratch/stefan/7774412/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=N2)S1) `REAL300004087772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087772 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 19, 27, 27, 14, 14, 11, 1, 11, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 14, 14, 14, 14, 19, 19, 14, 1, 1, 10, 10, 10, 10] 41 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087772 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 34, 34, 34, 34, 34, 1, 2, 2, 2, 2, 2, 2, 14, 14, 34, 34, 34, 34] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087772 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 41, 41, 41, 34, 34, 32, 10, 32, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 41, 41, 34, 10, 10, 1, 1, 1, 1] 41 rigid atoms, others: [32, 33, 34, 35, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087772 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087772 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087772/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087772 Building REAL300004087773 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087773' /scratch/stefan/7774412/working/building/REAL300004087773 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087773 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087773/0 /scratch/stefan/7774412/working/building/REAL300004087773 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/977 `/scratch/stefan/7774412/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)C=C2C)S1) `REAL300004087773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087773 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 21, 21, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 6, 6, 6, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 1, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2] 35 rigid atoms, others: [38, 10, 12, 13, 14, 15, 16, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087773 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 21, 21, 21, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 21, 21, 21, 21, 21, 21, 21, 9, 9, 9, 9] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087773 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCC3)C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 35, 35, 35, 21, 21, 21, 6, 21, 6, 6, 6, 1, 1, 1, 1, 1, 6, 6, 6, 21, 21, 21, 21, 35, 35, 21, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41]) total number of confs: 131 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087773 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087773 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087773/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087773 Building REAL300004087774 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087774' /scratch/stefan/7774412/working/building/REAL300004087774 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087774 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087774/0 /scratch/stefan/7774412/working/building/REAL300004087774 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/978 `/scratch/stefan/7774412/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CSC[C@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087774 none CC(=O)N1CSC[C@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 12, 15, 12, 12, 12, 12, 3, 12, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 15, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2] 25 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087774 none CC(=O)N1CSC[C@H]1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 12, 12, 12, 21, 21, 21, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 8, 21, 21, 12, 12, 12] 25 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087774 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087774/1 /scratch/stefan/7774412/working/building/REAL300004087774 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/979 `/scratch/stefan/7774412/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CSC[C@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087774.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087774/1/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: REAL300004087774 none CC(=O)N1CSC[C@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [107, 94, 107, 94, 94, 94, 94, 59, 94, 12, 59, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 107, 107, 107, 94, 94, 94, 94, 3, 3, 2, 2, 2] 135 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087774 none CC(=O)N1CSC[C@H]1C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 14, 5, 5, 7, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 94, 94, 94, 132, 133, 133, 94, 94, 94, 4, 4, 4, 1, 1, 1, 1, 132, 132, 94, 94, 94] 135 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087774 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087774 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087774/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087774/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087774 Building REAL300004087775 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087775' /scratch/stefan/7774412/working/building/REAL300004087775 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087775 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087775/0 /scratch/stefan/7774412/working/building/REAL300004087775 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/980 `/scratch/stefan/7774412/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1CC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CO2) `REAL300004087775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087775 none COC1=CC=CC2=C1CC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 23, 23, 23, 23, 23, 23, 23, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 23, 23, 37, 37, 37, 23, 23, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 23, 23] 49 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087775 none COC1=CC=CC2=C1CC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 14, 23, 23, 23, 43, 49, 49, 23, 23, 23, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 14, 43, 43, 23, 23, 23, 1, 1] 49 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 41, 23, 24, 33, 28, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087775 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087775/1 /scratch/stefan/7774412/working/building/REAL300004087775 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/981 `/scratch/stefan/7774412/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC2=C1CC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)CO2) `REAL300004087775.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087775/1/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: REAL300004087775 none COC1=CC=CC2=C1CC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 143, 143, 143, 143, 143, 143, 143, 143, 48, 13, 48, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 143, 143, 164, 164, 164, 143, 143, 143, 143, 143, 143, 2, 2, 2, 2, 2, 143, 143] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087775 none COC1=CC=CC2=C1CC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 57, 143, 143, 143, 184, 201, 201, 143, 143, 143, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 184, 184, 143, 143, 143, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 23, 24, 33, 28, 29, 30, 31] set([0, 34, 35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087775 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087775 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087775/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087775/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087775 Building REAL300004087776 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087776' /scratch/stefan/7774412/working/building/REAL300004087776 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087776 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087776/0 /scratch/stefan/7774412/working/building/REAL300004087776 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/982 `/scratch/stefan/7774412/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H]2C[C@@H](C(C)C)C3=CC=CC=C32)S1) `REAL300004087776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087776 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H]2C[C@@H](C(C)C)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 20, 20, 20, 14, 14, 12, 4, 12, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 20, 20, 14, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 24 rigid atoms, others: [48, 45, 36, 37, 46, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087776 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H]2C[C@@H](C(C)C)C3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 11, 14, 14, 14, 14, 14, 18, 18, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 11, 11, 14, 14, 18, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087776 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087776 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087776/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087776 Building REAL300004087777 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087777' /scratch/stefan/7774412/working/building/REAL300004087777 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087777 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087777/0 /scratch/stefan/7774412/working/building/REAL300004087777 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/983 `/scratch/stefan/7774412/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C(F)=CC=C3N2)S1) `REAL300004087777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087777 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C(F)=CC=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 15, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 13, 25, 25, 25, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 25, 25, 8, 1, 2, 2, 2, 1, 1, 1] 25 rigid atoms, others: [34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087777 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C(F)=CC=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 15, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 13, 13, 13, 12, 12, 12] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087777 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087777 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087777/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087777 Building REAL300004087778 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087778' /scratch/stefan/7774412/working/building/REAL300004087778 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087778 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087778/0 /scratch/stefan/7774412/working/building/REAL300004087778 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/984 `/scratch/stefan/7774412/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=NC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087778 none COC1=CC=NC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087778 none COC1=CC=NC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 8, 11, 11, 11, 19, 19, 19, 11, 11, 11, 3, 3, 3, 1, 1, 1, 8, 19, 19, 11, 11, 11] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087778 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087778 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087778/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087778 Building REAL300004087779 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087779' /scratch/stefan/7774412/working/building/REAL300004087779 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087779 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087779/0 /scratch/stefan/7774412/working/building/REAL300004087779 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/985 `/scratch/stefan/7774412/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCNC(=O)C3=C2)S1) `REAL300004087779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087779 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCNC(=O)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 14, 14, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 7, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087779 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCNC(=O)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087779 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087779 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087779/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087779 Building REAL300004087780 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087780' /scratch/stefan/7774412/working/building/REAL300004087780 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087780 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087780/0 /scratch/stefan/7774412/working/building/REAL300004087780 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/986 `/scratch/stefan/7774412/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CN=C3C=C2C)S1) `REAL300004087780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087780 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CN=C3C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 17, 17, 17, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 8, 1, 1, 1, 1, 2, 2, 2] 17 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 35, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087780 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=NC=CN=C3C=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087780 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087780 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087780/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087780 Building REAL300004087781 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087781' /scratch/stefan/7774412/working/building/REAL300004087781 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087781 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087781/0 /scratch/stefan/7774412/working/building/REAL300004087781 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/987 `/scratch/stefan/7774412/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C(Cl)=CC=C3N2)S1) `REAL300004087781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087781 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C(Cl)=CC=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 13, 25, 25, 25, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 24, 25, 8, 1, 2, 2, 2, 1, 1, 1] 25 rigid atoms, others: [34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087781 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C(Cl)=CC=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 16, 1, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 13, 13, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087781 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087781 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087781/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087781 Building REAL300004087782 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087782' /scratch/stefan/7774412/working/building/REAL300004087782 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087782 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087782/0 /scratch/stefan/7774412/working/building/REAL300004087782 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/988 `/scratch/stefan/7774412/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1) `REAL300004087782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087782 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 3, 3, 1, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [37, 38, 39, 40, 10, 12, 13, 14, 15, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087782 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 2, 3, 3, 3, 2, 2, 2, 2, 1, 2, 2, 2, 1, 1, 2, 3, 3, 3, 3, 2, 2, 2, 2] 3 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 26, 30, 31] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087782 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 4 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087782 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087782/1 /scratch/stefan/7774412/working/building/REAL300004087782 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/989 `/scratch/stefan/7774412/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1) `REAL300004087782.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087782 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 160, 164, 164, 119, 36, 11, 1, 11, 1, 1, 1, 1, 5, 5, 2, 3, 5, 5, 1, 1, 1, 1, 119, 119, 119, 119, 160, 160, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 14, 15, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 447 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087782 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 12, 51, 51, 119, 119, 119, 174, 174, 147, 161, 174, 174, 119, 119, 119, 119, 1, 2, 2, 2, 3, 3, 174, 174, 174, 174, 119, 119, 119, 119] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 438 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087782 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(F)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 174, 201, 201, 201, 174, 83, 31, 5, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 174, 174, 174, 174, 201, 201, 1, 1, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 444 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087782 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087782 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087782/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087782/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087782 Building REAL300004087783 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087783' /scratch/stefan/7774412/working/building/REAL300004087783 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087783 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087783/0 /scratch/stefan/7774412/working/building/REAL300004087783 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/990 `/scratch/stefan/7774412/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1) `REAL300004087783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087783 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 4, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 4, 4, 3, 3, 4, 4, 1, 1, 1, 1, 3, 4, 4, 4, 4, 5, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 6 rigid atoms, others: [40, 41, 10, 43, 12, 13, 14, 15, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087783 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 3, 3, 4, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3] 6 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087783 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 6, 6, 6, 5, 5, 5, 4, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 6, 6, 5, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4] 6 rigid atoms, others: [33, 34, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 21 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087783 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087783/1 /scratch/stefan/7774412/working/building/REAL300004087783 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/991 `/scratch/stefan/7774412/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1) `REAL300004087783.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087783/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087783 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 163, 168, 168, 122, 36, 11, 1, 11, 1, 1, 1, 1, 5, 5, 3, 3, 5, 5, 1, 1, 1, 1, 122, 122, 122, 122, 163, 163, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 10, 12, 13, 14, 15, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 461 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087783 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 55, 55, 122, 122, 122, 172, 172, 163, 163, 172, 172, 122, 122, 122, 122, 1, 2, 2, 2, 3, 3, 172, 172, 172, 172, 172, 172, 172, 122, 122, 122, 122] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 427 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087783 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=NN(C3=CC=C(C)C=C3)C(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 80, 31, 5, 31, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 172, 172, 172, 172, 201, 201, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5] 201 rigid atoms, others: [32, 33, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 457 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087783 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087783 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087783/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087783/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087783 Building REAL300004087784 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087784' /scratch/stefan/7774412/working/building/REAL300004087784 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087784 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087784/0 /scratch/stefan/7774412/working/building/REAL300004087784 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/992 `/scratch/stefan/7774412/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)OC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087784 none CC1=C(C)OC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 26, 16, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 26, 26, 16, 16, 2, 2, 2, 2, 2, 2] 97 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087784 none CC1=C(C)OC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 23, 59, 59, 63, 65, 65, 65, 97, 97, 97, 65, 65, 65, 1, 2, 2, 2, 2, 2, 2, 9, 9, 23, 23, 63, 97, 97, 65, 65, 65] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087784 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087784 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087784/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087784 Building REAL300004087785 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087785' /scratch/stefan/7774412/working/building/REAL300004087785 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087785 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087785/0 /scratch/stefan/7774412/working/building/REAL300004087785 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/993 `/scratch/stefan/7774412/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCN1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087785 none COCCOCCN1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 137, 107, 68, 44, 30, 9, 9, 9, 9, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 139, 139, 139, 137, 137, 107, 107, 44, 44, 30, 30, 9, 9, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [13, 14, 15, 16, 17, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087785 none COCCOCCN1C=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 65, 47, 24, 10, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 15, 33, 33, 9, 9, 9, 1, 69, 69, 69, 65, 65, 47, 47, 10, 10, 6, 6, 1, 1, 6, 15, 15, 9, 9, 9] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 381 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087785 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087785 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087785/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087785 Building REAL300004087786 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087786' /scratch/stefan/7774412/working/building/REAL300004087786 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087786 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087786/0 /scratch/stefan/7774412/working/building/REAL300004087786 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/994 `/scratch/stefan/7774412/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCN1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087786 none COCCOCCN1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 129, 107, 44, 16, 16, 7, 7, 7, 7, 7, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 139, 139, 139, 129, 129, 107, 107, 16, 16, 16, 16, 7, 7, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 541 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087786 none COCCOCCN1N=CC=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 62, 48, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 11, 21, 21, 7, 7, 7, 75, 75, 75, 62, 62, 48, 48, 6, 6, 6, 6, 1, 1, 4, 11, 11, 7, 7, 7] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087786 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087786 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087786/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087786 Building REAL300004087787 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087787' /scratch/stefan/7774412/working/building/REAL300004087787 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087787 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087787/0 /scratch/stefan/7774412/working/building/REAL300004087787 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/995 `/scratch/stefan/7774412/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CCC3=CC=CC=C3)C=C2)S1) `REAL300004087787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087787 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CCC3=CC=CC=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 11, 13, 13, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 10, 14, 14, 10, 14, 14, 1, 1, 6, 6, 6, 6, 11, 11, 4, 1, 1, 6, 6, 10, 10, 15, 15, 10, 15, 15, 1, 1] 68 rigid atoms, others: [33, 34, 44, 10, 45, 12, 13, 14, 15, 16, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087787 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CCC3=CC=CC=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 21, 36, 40, 40, 36, 40, 40, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 21, 21, 36, 36, 40, 40, 36, 40, 40, 6, 6] 68 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087787 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CCC3=CC=CC=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 68, 68, 68, 40, 31, 31, 14, 31, 14, 14, 14, 5, 3, 1, 1, 1, 1, 1, 1, 1, 14, 14, 40, 40, 40, 40, 68, 68, 31, 14, 14, 5, 5, 3, 3, 1, 1, 1, 1, 1, 14, 14] 68 rigid atoms, others: [39, 40, 41, 42, 43, 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, 44, 45]) total number of confs: 277 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087787 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087787 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087787/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087787 Building REAL300004087788 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087788' /scratch/stefan/7774412/working/building/REAL300004087788 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087788 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087788/0 /scratch/stefan/7774412/working/building/REAL300004087788 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/996 `/scratch/stefan/7774412/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3CCCC3=NNC2=O)S1) `REAL300004087788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087788 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3CCCC3=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087788 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3CCCC3=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087788 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087788/1 /scratch/stefan/7774412/working/building/REAL300004087788 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/997 `/scratch/stefan/7774412/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=C3CCCC3=NNC2=O)S1) `REAL300004087788.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087788/1/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: REAL300004087788 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=C3CCCC3=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 201, 201, 201, 161, 51, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 465 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087788 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=C3CCCC3=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 76, 76, 161, 161, 161, 161, 161, 161, 161, 161, 161, 1, 2, 2, 2, 2, 2, 161, 161, 161, 161, 161, 161, 160] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087788 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087788 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087788/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087788/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087788 Building REAL300004087789 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087789' /scratch/stefan/7774412/working/building/REAL300004087789 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087789 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087789/0 /scratch/stefan/7774412/working/building/REAL300004087789 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/998 `/scratch/stefan/7774412/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CSC=C3)N=C2)S1) `REAL300004087789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087789 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CSC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 11, 11, 11, 11, 19, 19, 7, 1, 1, 9, 9, 9, 1] 55 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087789 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CSC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 44, 44, 44, 44, 11, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 44, 44, 44, 11] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087789 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CSC=C3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 55, 55, 55, 44, 37, 37, 9, 37, 9, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 44, 44, 44, 44, 55, 55, 37, 9, 9, 1, 1, 1, 9] 55 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087789 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087789 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087789/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087789 Building REAL300004087790 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087790' /scratch/stefan/7774412/working/building/REAL300004087790 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087790 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087790/0 /scratch/stefan/7774412/working/building/REAL300004087790 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/999 `/scratch/stefan/7774412/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@@H]2CCC[C@H](C3CC3)O2)S1) `REAL300004087790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087790 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@@H]2CCC[C@H](C3CC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 26, 26, 42, 44, 44, 26, 25, 23, 7, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 1, 26, 26, 26, 26, 42, 42, 25, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 67 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087790 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@@H]2CCC[C@H](C3CC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 15, 26, 26, 26, 26, 26, 26, 26, 44, 44, 26, 1, 2, 2, 2, 2, 2, 2, 15, 15, 26, 26, 26, 26, 26, 26, 44, 44, 44, 44, 44] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087790 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@@H]2CCC[C@H](C3CC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 5, 5, 5, 7, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 67, 67, 67, 44, 43, 40, 16, 40, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 7, 44, 44, 44, 44, 67, 67, 43, 16, 16, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1] 67 rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 266 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087790 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087790 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087790/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087790 Building REAL300004087791 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087791' /scratch/stefan/7774412/working/building/REAL300004087791 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087791 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087791/0 /scratch/stefan/7774412/working/building/REAL300004087791 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1000 `/scratch/stefan/7774412/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1) `REAL300004087791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087791 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 127, 129, 129, 67, 48, 45, 11, 45, 6, 1, 1, 1, 1, 1, 1, 1, 11, 18, 18, 15, 18, 18, 67, 67, 67, 67, 127, 127, 48, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18] 129 rigid atoms, others: [45, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46] 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, 47, 48, 49, 50, 51]) total number of confs: 573 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087791 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 21, 52, 67, 67, 67, 67, 67, 21, 36, 36, 27, 36, 36, 1, 2, 2, 2, 2, 2, 2, 21, 52, 52, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 36, 36, 35, 36, 36] 129 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 350 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087791 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 36, 36, 69, 82, 82, 36, 23, 22, 4, 22, 1, 4, 8, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 36, 36, 36, 36, 69, 69, 23, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1] 129 rigid atoms, others: [12, 47, 48, 49, 50, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 383 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087791 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087791/1 /scratch/stefan/7774412/working/building/REAL300004087791 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1001 `/scratch/stefan/7774412/working/3D/1001' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1) `REAL300004087791.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087791 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 195, 201, 201, 138, 45, 16, 7, 16, 4, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 138, 138, 138, 138, 195, 195, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 201 rigid atoms, others: [45, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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, 46, 47, 48, 49, 50]) total number of confs: 590 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087791 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 52, 52, 87, 127, 138, 138, 138, 138, 138, 87, 105, 105, 105, 105, 105, 1, 2, 2, 2, 2, 2, 87, 127, 127, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 105, 105, 105, 105, 105] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 619 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087791 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(CC2CCCCC2)C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 154, 160, 160, 105, 30, 8, 3, 8, 1, 3, 8, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 154, 154, 3, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1] 201 rigid atoms, others: [12, 46, 47, 48, 49, 50, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 500 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087791 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087791 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087791/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087791/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087791 Building REAL300004087792 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087792' /scratch/stefan/7774412/working/building/REAL300004087792 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087792 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087792/0 /scratch/stefan/7774412/working/building/REAL300004087792 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1002 `/scratch/stefan/7774412/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C(C)C2=CC=CC=C2Cl)S1) `REAL300004087792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087792 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C(C)C2=CC=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 24, 24, 24, 18, 13, 13, 5, 13, 2, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 24, 24, 13, 5, 5, 6, 6, 2, 2, 2, 2, 1, 1, 1, 1] 24 rigid atoms, others: [38, 39, 40, 41, 14, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087792 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C(C)C2=CC=CC=C2Cl)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 11, 17, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087792 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087792 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087792/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087792 Building REAL300004087793 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087793' /scratch/stefan/7774412/working/building/REAL300004087793 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087793 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087793/0 /scratch/stefan/7774412/working/building/REAL300004087793 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1003 `/scratch/stefan/7774412/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CCC3)C=C2)S1) `REAL300004087793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087793 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 13, 15, 15, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 11, 11, 11, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 1, 1] 65 rigid atoms, others: [41, 10, 12, 13, 14, 15, 16, 21, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087793 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 21, 33, 33, 33, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 33, 33, 33, 33, 33, 33, 33, 7, 7] 65 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087793 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CC3CCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 65, 65, 65, 33, 25, 23, 11, 23, 5, 11, 11, 5, 1, 1, 1, 1, 1, 11, 11, 33, 33, 33, 33, 65, 65, 25, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11] 65 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42]) total number of confs: 306 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087793 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087793 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087793/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087793 Building REAL300004087794 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087794' /scratch/stefan/7774412/working/building/REAL300004087794 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087794 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087794/0 /scratch/stefan/7774412/working/building/REAL300004087794 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1004 `/scratch/stefan/7774412/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC3=CC=CN=C3C=C2)S1) `REAL300004087794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087794 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC3=CC=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 19, 19, 19, 13, 13, 13, 5, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 19, 19, 13, 5, 5, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 71 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087794 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC3=CC=CN=C3C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 13] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087794 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087794 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087794/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087794 Building REAL300004087795 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087795' /scratch/stefan/7774412/working/building/REAL300004087795 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087795 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087795/0 /scratch/stefan/7774412/working/building/REAL300004087795 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1005 `/scratch/stefan/7774412/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)[C@@H]2CCC[C@H](C(F)(F)F)N2)S1) `REAL300004087795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087795 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)[C@@H]2CCC[C@H](C(F)(F)F)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 10, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 30, 30, 30, 16, 13, 13, 6, 13, 1, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 30, 30, 13, 6, 6, 6, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [40, 41, 42, 43, 12, 45, 46, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087795 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)[C@@H]2CCC[C@H](C(F)(F)F)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 10, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087795 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087795/1 /scratch/stefan/7774412/working/building/REAL300004087795 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1006 `/scratch/stefan/7774412/working/3D/1006' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)[C@@H]2CCC[C@H](C(F)(F)F)N2)S1) `REAL300004087795.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087795/1/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: REAL300004087795 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)[C@@H]2CCC[C@H](C(F)(F)F)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 10, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 126, 126, 126, 96, 31, 9, 3, 9, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 126, 126, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1] 126 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 321 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087795 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)[C@@H]2CCC[C@H](C(F)(F)F)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 5, 15, 15, 15, 10, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 42, 42, 94, 94, 94, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 2, 2, 2, 2, 2, 94, 94, 94, 94, 94, 94, 96, 96, 96, 96, 96, 96, 96] 126 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 368 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087795 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087795 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087795/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087795/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087795 Building REAL300004087796 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087796' /scratch/stefan/7774412/working/building/REAL300004087796 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087796 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087796/0 /scratch/stefan/7774412/working/building/REAL300004087796 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1007 `/scratch/stefan/7774412/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C)OC(C)(C)C2)S1) `REAL300004087796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087796 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C)OC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 36, 37, 37, 18, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 36, 36, 12, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1] 37 rigid atoms, others: [45, 44, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087796 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C)OC(C)(C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 18] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087796 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087796 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087796/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087796 Building REAL300004087797 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087797' /scratch/stefan/7774412/working/building/REAL300004087797 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087797 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087797/0 /scratch/stefan/7774412/working/building/REAL300004087797 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1008 `/scratch/stefan/7774412/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23OC4C5COCC4C2C53)S1) `REAL300004087797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087797 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23OC4C5COCC4C2C53)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087797 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23OC4C5COCC4C2C53)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087797 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087797/1 /scratch/stefan/7774412/working/building/REAL300004087797 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1009 `/scratch/stefan/7774412/working/3D/1009' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23OC4C5COCC4C2C53)S1) `REAL300004087797.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087797/1/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: REAL300004087797 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23OC4C5COCC4C2C53)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 201, 201, 201, 162, 70, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 458 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087797 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23OC4C5COCC4C2C53)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 56, 56, 162, 162, 162, 162, 162, 162, 162, 162, 162, 1, 2, 2, 2, 2, 2, 162, 162, 162, 162, 162, 162, 162, 162, 162] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087797 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087797 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087797/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087797/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087797 Building REAL300004087798 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087798' /scratch/stefan/7774412/working/building/REAL300004087798 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087798 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087798/0 /scratch/stefan/7774412/working/building/REAL300004087798 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1010 `/scratch/stefan/7774412/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCOCC2)S1) `REAL300004087798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087798 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 1, 3, 1, 1, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 12, 13, 44, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087798 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 5, 7, 7, 7, 7, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087798 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 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 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 5, 5, 4, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 7, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 13 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087798 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087798/1 /scratch/stefan/7774412/working/building/REAL300004087798 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1011 `/scratch/stefan/7774412/working/3D/1011' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCOCC2)S1) `REAL300004087798.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087798 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 6, 3, 1, 3, 1, 1, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 28 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087798 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 38 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087798 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 7, 6, 5, 6, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 21 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087798 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087798 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087798/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087798/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087798 Building REAL300004087799 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087799' /scratch/stefan/7774412/working/building/REAL300004087799 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087799 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087799/0 /scratch/stefan/7774412/working/building/REAL300004087799 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1012 `/scratch/stefan/7774412/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3CC[C@@H](C3)[C@H]2C2=CC=CC=C2)S1) `REAL300004087799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087799 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3CC[C@@H](C3)[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 9, 9, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2] 9 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087799 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3CC[C@@H](C3)[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 29] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 37 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087799 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3CC[C@@H](C3)[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 4, 3, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 4, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 45, 46, 21, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087799 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087799 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087799/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087799 Building REAL300004087800 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087800' /scratch/stefan/7774412/working/building/REAL300004087800 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087800 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087800/0 /scratch/stefan/7774412/working/building/REAL300004087800 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1013 `/scratch/stefan/7774412/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC(O)=CC(Br)=C2)S1) `REAL300004087800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087800 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC(O)=CC(Br)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 12, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 74, 74, 74, 38, 22, 21, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 74, 74, 22, 7, 7, 1, 2, 1, 1] 148 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 316 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087800 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC(O)=CC(Br)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 12, 1, 1, 17, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 10, 38, 38, 38, 38, 38, 38, 38, 1, 2, 2, 2, 3, 3, 2, 10, 10, 38, 76, 38, 38] 148 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087800 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087800 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087800/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087800 Building REAL300004087801 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087801' /scratch/stefan/7774412/working/building/REAL300004087801 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087801 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087801/0 /scratch/stefan/7774412/working/building/REAL300004087801 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1014 `/scratch/stefan/7774412/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCC2=CC=CC(O)=C2)S1) `REAL300004087801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087801 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCC2=CC=CC(O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [39, 40, 40, 40, 70, 70, 70, 40, 40, 38, 24, 37, 20, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 39, 40, 40, 40, 70, 70, 40, 29, 29, 24, 24, 13, 13, 7, 7, 1, 1, 1, 2, 1] 140 rigid atoms, others: [38, 39, 40, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087801 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCCCC2=CC=CC(O)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 9, 13, 15, 39, 39, 39, 39, 40, 39, 1, 2, 2, 2, 2, 2, 2, 8, 8, 11, 11, 13, 13, 15, 15, 40, 40, 39, 80, 40] 140 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087801 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087801 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087801/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087801 Building REAL300004087802 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087802' /scratch/stefan/7774412/working/building/REAL300004087802 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087802 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087802/0 /scratch/stefan/7774412/working/building/REAL300004087802 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1015 `/scratch/stefan/7774412/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1) `REAL300004087802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087802 none CC1=NC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 6, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 2, 2, 2, 2, 2, 2] 9 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087802 none CC1=NC=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 7, 7, 7, 7, 9, 9, 9, 7, 7, 7, 1, 2, 2, 2, 1, 2, 2, 7, 9, 9, 7, 7, 7] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087802 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087802 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087802/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087802 Building REAL300004087803 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087803' /scratch/stefan/7774412/working/building/REAL300004087803 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087803 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087803/0 /scratch/stefan/7774412/working/building/REAL300004087803 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1016 `/scratch/stefan/7774412/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(Cl)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087803 none CCC1=NC=C(Cl)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 7, 7, 7, 7, 7, 3, 2, 2, 2, 1, 1, 1] 9 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087803 none CCC1=NC=C(Cl)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 16, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 7, 7, 3, 3, 3, 1, 5, 5, 5, 5, 5, 1, 3, 5, 5, 3, 3, 3] 9 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 27] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087803 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087803 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087803/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087803 Building REAL300004087804 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087804' /scratch/stefan/7774412/working/building/REAL300004087804 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087804 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087804/0 /scratch/stefan/7774412/working/building/REAL300004087804 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1017 `/scratch/stefan/7774412/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2)S1) `REAL300004087804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087804 none CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 15, 15, 15, 15, 14, 15, 2, 2, 2, 2, 2, 2, 14] 25 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087804 none CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 10, 15, 15, 15, 25, 25, 25, 14, 14, 14, 1, 1, 2, 2, 2, 1, 1, 10, 25, 25, 15, 15, 15, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 33, 20, 21, 25, 26] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087804 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087804 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087804/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087804 Building REAL300004087805 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087805' /scratch/stefan/7774412/working/building/REAL300004087805 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087805 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087805/0 /scratch/stefan/7774412/working/building/REAL300004087805 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1018 `/scratch/stefan/7774412/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC3(C)C)S1) `REAL300004087805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087805 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 5, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2] 17 rigid atoms, others: [33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087805 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087805 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087805/1 /scratch/stefan/7774412/working/building/REAL300004087805 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1019 `/scratch/stefan/7774412/working/3D/1019' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC3(C)C)S1) `REAL300004087805.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087805/1/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: REAL300004087805 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 201, 201, 201, 133, 35, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 201, 201, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087805 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 54, 54, 133, 133, 133, 133, 133, 133, 133, 133, 1, 2, 2, 2, 2, 2, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133, 133] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087805 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087805 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087805/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087805/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087805 Building REAL300004087806 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087806' /scratch/stefan/7774412/working/building/REAL300004087806 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087806 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087806/0 /scratch/stefan/7774412/working/building/REAL300004087806 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1020 `/scratch/stefan/7774412/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)N2C=NN=N2)S1) `REAL300004087806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087806 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)N2C=NN=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 8, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 115, 115, 115, 71, 51, 51, 13, 51, 1, 13, 13, 1, 1, 1, 1, 1, 71, 71, 71, 71, 115, 115, 51, 13, 13, 13, 13, 13, 13, 1] 115 rigid atoms, others: [33, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 444 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087806 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)N2C=NN=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 8, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 24, 24, 24, 71, 71, 71, 71, 1, 2, 2, 2, 2, 2, 2, 25, 25, 25, 25, 25, 25, 71] 115 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087806 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087806/1 /scratch/stefan/7774412/working/building/REAL300004087806 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1021 `/scratch/stefan/7774412/working/3D/1021' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)N2C=NN=N2)S1) `REAL300004087806.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087806/1/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: REAL300004087806 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)N2C=NN=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 8, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 9, 17, 1, 9, 9, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 1] 19 rigid atoms, others: [32, 12, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087806 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)N2C=NN=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 8, 1, 8, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 8, 13, 13, 15, 15, 15, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 19] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087806 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087806 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087806/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087806/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087806 Building REAL300004087807 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087807' /scratch/stefan/7774412/working/building/REAL300004087807 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087807 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087807/0 /scratch/stefan/7774412/working/building/REAL300004087807 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1022 `/scratch/stefan/7774412/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=CN=CN=C2)S1) `REAL300004087807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087807 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=CN=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 70, 70, 70, 39, 24, 24, 10, 24, 1, 10, 10, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 70, 70, 24, 10, 10, 10, 10, 10, 10, 1, 1, 1] 70 rigid atoms, others: [34, 35, 36, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 285 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087807 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)(C)C2=CN=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 23, 23, 23, 39, 39, 23, 39, 39, 1, 2, 2, 2, 3, 3, 2, 23, 23, 23, 23, 23, 23, 39, 23, 39] 70 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087807 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087807/1 /scratch/stefan/7774412/working/building/REAL300004087807 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1023 `/scratch/stefan/7774412/working/3D/1023' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=CN=CN=C2)S1) `REAL300004087807.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087807/1/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: REAL300004087807 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=CN=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 89, 33, 9, 33, 1, 9, 9, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 201, 201, 9, 9, 9, 9, 9, 9, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 12, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087807 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)(C)C2=CN=CN=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 8, 1, 8, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 36, 36, 120, 120, 120, 166, 166, 120, 166, 166, 1, 2, 2, 2, 2, 2, 120, 120, 120, 120, 120, 120, 166, 120, 166] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 677 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087807 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087807 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087807/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087807/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087807 Building REAL300004087808 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087808' /scratch/stefan/7774412/working/building/REAL300004087808 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087808 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087808/0 /scratch/stefan/7774412/working/building/REAL300004087808 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1024 `/scratch/stefan/7774412/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCC2)S1) `REAL300004087808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087808 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 11, 11, 6, 4, 4, 1, 4, 1, 1, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 18, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 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: REAL300004087808 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 6, 8, 8, 8, 8, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 47 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087808 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 6, 6, 4, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 8, 8, 8, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4] 15 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 61 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087808 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087808/1 /scratch/stefan/7774412/working/building/REAL300004087808 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1025 `/scratch/stefan/7774412/working/3D/1025' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCC2)S1) `REAL300004087808.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087808 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 5, 3, 1, 3, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 8 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 18, 19, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087808 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 6, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 8 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087808 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 5, 4, 3, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3] 8 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 18 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087808 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087808 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087808/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087808/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087808 Building REAL300004087809 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087809' /scratch/stefan/7774412/working/building/REAL300004087809 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087809 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087809/0 /scratch/stefan/7774412/working/building/REAL300004087809 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1026 `/scratch/stefan/7774412/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC=CC1) `REAL300004087809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087809 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 10, 2, 3, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 24, 24, 3, 2, 2, 1, 1, 1, 10, 10, 10, 10, 10, 10] 45 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 113 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087809 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 1, 1, 1, 7, 7, 7, 10, 10, 10, 19, 19, 19, 10, 10, 10, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 19, 19, 10, 10, 10, 1, 1, 1, 1, 1, 1] 45 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 34, 17, 18, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 95 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087809 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087809/1 /scratch/stefan/7774412/working/building/REAL300004087809 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1027 `/scratch/stefan/7774412/working/3D/1027' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CC=CC1) `REAL300004087809.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087809/1/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: REAL300004087809 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 148, 127, 48, 12, 48, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 127, 127, 127, 127, 169, 169, 169, 148, 148, 2, 2, 1, 1, 1, 127, 127, 127, 127, 127, 127] 201 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087809 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 1, 1, 1, 7, 7, 34, 127, 127, 127, 184, 191, 191, 127, 127, 127, 1, 1, 1, 1, 12, 12, 12, 5, 5, 184, 184, 127, 127, 127, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 17, 18, 19, 20, 36, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087809 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087809 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087809/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087809/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087809 Building REAL300004087810 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087810' /scratch/stefan/7774412/working/building/REAL300004087810 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087810 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087810/0 /scratch/stefan/7774412/working/building/REAL300004087810 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1028 `/scratch/stefan/7774412/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2CSC3)S1) `REAL300004087810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087810 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2CSC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 5, 14, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [18, 19, 19, 19, 30, 30, 30, 19, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 30, 30, 13, 1, 1, 1, 1, 1] 30 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 114 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087810 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C2CSC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.3', 'S.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 5, 14, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 1, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19] 30 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087810 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087810 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087810/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087810 Building REAL300004087811 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087811' /scratch/stefan/7774412/working/building/REAL300004087811 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087811 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087811/0 /scratch/stefan/7774412/working/building/REAL300004087811 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1029 `/scratch/stefan/7774412/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CC=C(C(C)(C)C)C=C2)S1) `REAL300004087811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087811 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CC=C(C(C)(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 126, 188, 188, 70, 52, 47, 8, 47, 4, 7, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 70, 70, 70, 70, 126, 126, 52, 8, 8, 8, 8, 4, 4, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 188 rigid atoms, others: [49, 38, 39, 50, 14, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 778 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087811 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)CC2=CC=C(C(C)(C)C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 20, 20, 63, 70, 70, 67, 70, 109, 109, 109, 70, 70, 1, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 63, 63, 70, 70, 109, 109, 109, 109, 109, 109, 109, 109, 109, 70, 70] 188 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 544 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087811 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087811 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087811/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087811 Building REAL300004087812 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087812' /scratch/stefan/7774412/working/building/REAL300004087812 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087812 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087812/0 /scratch/stefan/7774412/working/building/REAL300004087812 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1030 `/scratch/stefan/7774412/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(Cl)C=C3)=C2)S1) `REAL300004087812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087812 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(Cl)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 27, 34, 34, 14, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 1, 1, 4, 4, 1, 14, 14, 14, 14, 27, 27, 11, 2, 2, 2, 4, 4, 4, 4, 1] 34 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 17, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087812 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(Cl)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 21, 21, 14, 14, 21, 21, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 21, 21, 21, 21, 14] 34 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087812 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C)C(C3=CC=C(Cl)C=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 34, 34, 34, 21, 16, 16, 4, 16, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 34, 34, 16, 4, 4, 4, 1, 1, 1, 1, 4] 34 rigid atoms, others: [35, 36, 37, 38, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 123 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087812 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087812 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087812/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087812 Building REAL300004087813 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087813' /scratch/stefan/7774412/working/building/REAL300004087813 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087813 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087813/0 /scratch/stefan/7774412/working/building/REAL300004087813 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1031 `/scratch/stefan/7774412/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC=C(C)C=C23)S1) `REAL300004087813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087813 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC=C(C)C=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 17, 33, 33, 33, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 33, 33, 11, 1, 1, 1, 2, 2, 2, 1] 33 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087813 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC=C(C)C=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 17, 17, 17, 17, 16, 1, 2, 2, 2, 2, 2, 2, 17, 16, 17, 17, 17, 17, 17] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087813 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087813 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087813/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087813 Building REAL300004087814 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087814' /scratch/stefan/7774412/working/building/REAL300004087814 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087814 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087814/0 /scratch/stefan/7774412/working/building/REAL300004087814 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1032 `/scratch/stefan/7774412/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SCCCC3=C2)S1) `REAL300004087814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087814 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087814 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087814 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087814 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087814/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087814 Building REAL300004087815 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087815' /scratch/stefan/7774412/working/building/REAL300004087815 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087815 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087815/0 /scratch/stefan/7774412/working/building/REAL300004087815 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1033 `/scratch/stefan/7774412/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SCCCCC3=C2)S1) `REAL300004087815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087815 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SCCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 24, 24, 24, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087815 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3SCCCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 5, 5, 5, 5, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087815 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087815 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087815/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087815 Building REAL300004087816 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087816' /scratch/stefan/7774412/working/building/REAL300004087816 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087816 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087816/0 /scratch/stefan/7774412/working/building/REAL300004087816 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1034 `/scratch/stefan/7774412/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1F) `REAL300004087816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087816 none CC(C)=CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 59, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 5, 13, 91, 91, 91, 91, 91, 91, 91, 59, 59, 13, 2, 2, 2, 2, 2, 2, 13, 13] 160 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 369 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087816 none CC(C)=CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 8, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 35, 35, 13, 13, 13, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 8, 8, 1, 9, 25, 25, 13, 13, 13, 1, 1] 160 rigid atoms, others: [34, 4, 5, 6, 7, 8, 41, 42, 21, 22, 23, 24] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40]) total number of confs: 197 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087816 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087816 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087816/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087816 Building REAL300004087817 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087817' /scratch/stefan/7774412/working/building/REAL300004087817 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087817 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087817/0 /scratch/stefan/7774412/working/building/REAL300004087817 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1035 `/scratch/stefan/7774412/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C(Cl)S3)N2)S1) `REAL300004087817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087817 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C(Cl)S3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 14, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [14, 15, 15, 15, 25, 25, 25, 15, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 25, 25, 11, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087817 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C(Cl)S3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 16, 14, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087817 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087817 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087817/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087817 Building REAL300004087818 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087818' /scratch/stefan/7774412/working/building/REAL300004087818 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087818 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087818/0 /scratch/stefan/7774412/working/building/REAL300004087818 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1036 `/scratch/stefan/7774412/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CN=C3)=N2)S1) `REAL300004087818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087818 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CN=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 13, 23, 29, 29, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 13, 13, 12, 13, 13, 1, 12, 13, 13, 13, 22, 23, 9, 1, 1, 13, 13, 12, 13] 63 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36]) 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: REAL300004087818 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CN=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 41, 41, 41, 41, 41, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 41, 41, 41, 41] 63 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087818 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=NC(C3=CC=CN=C3)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 63, 63, 63, 41, 33, 33, 13, 33, 13, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 41, 41, 41, 41, 63, 63, 33, 12, 13, 1, 1, 1, 1] 63 rigid atoms, others: [33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 221 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087818 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087818 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087818/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087818 Building REAL300004087819 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087819' /scratch/stefan/7774412/working/building/REAL300004087819 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087819 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087819/0 /scratch/stefan/7774412/working/building/REAL300004087819 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1037 `/scratch/stefan/7774412/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC3=CC=CC=C3N=C2)S1) `REAL300004087819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087819 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC3=CC=CC=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 73, 73, 73, 37, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 73, 73, 21, 6, 6, 1, 1, 1, 1, 1, 1] 73 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 309 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087819 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC3=CC=CC=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 2, 2, 2, 9, 9, 37, 37, 37, 37, 37, 37] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087819 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087819 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087819/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087819 Building REAL300004087820 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087820' /scratch/stefan/7774412/working/building/REAL300004087820 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087820 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087820/0 /scratch/stefan/7774412/working/building/REAL300004087820 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1038 `/scratch/stefan/7774412/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC(C)=CC=C23)S1) `REAL300004087820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087820 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC(C)=CC=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 30, 31, 31, 16, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 30, 30, 11, 1, 1, 2, 2, 2, 1, 1] 31 rigid atoms, others: [34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 22, 23, 24, 25, 26, 27, 28, 31]) 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: REAL300004087820 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC(C)=CC=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 17, 17, 17, 16, 16] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087820 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087820 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087820/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087820 Building REAL300004087821 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087821' /scratch/stefan/7774412/working/building/REAL300004087821 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087821 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087821/0 /scratch/stefan/7774412/working/building/REAL300004087821 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1039 `/scratch/stefan/7774412/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NC(C(C)(C)C)=N2)S1) `REAL300004087821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087821 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 1, 5, 5, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 22, 22, 22, 15, 15, 15, 8, 15, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 15, 15, 15, 15, 22, 22, 15, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 118 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087821 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 1, 5, 5, 5, 5, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 6, 15, 15, 15, 15, 27, 27, 27, 15, 1, 2, 2, 2, 2, 2, 2, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087821 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087821/1 /scratch/stefan/7774412/working/building/REAL300004087821 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1040 `/scratch/stefan/7774412/working/3D/1040' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NC(C(C)(C)C)=N2)S1) `REAL300004087821.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087821/1/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: REAL300004087821 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 123, 127, 127, 98, 58, 30, 8, 30, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 98, 98, 98, 98, 123, 123, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087821 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 26, 26, 47, 98, 98, 98, 98, 172, 172, 172, 98, 1, 2, 2, 2, 2, 2, 47, 47, 172, 172, 172, 172, 172, 172, 172, 172, 172] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 687 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087821 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087821 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087821/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087821/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087821 Building REAL300004087822 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087822' /scratch/stefan/7774412/working/building/REAL300004087822 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087822 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087822/0 /scratch/stefan/7774412/working/building/REAL300004087822 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1041 `/scratch/stefan/7774412/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CS3)N2CC2CC2)S1) `REAL300004087822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087822 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CS3)N2CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 35, 59, 59, 20, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 20, 20, 20, 20, 35, 35, 12, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12] 88 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 258 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087822 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CS3)N2CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 40, 64, 64, 1, 2, 2, 2, 2, 2, 2, 20, 20, 20, 40, 40, 64, 64, 64, 64, 64] 88 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087822 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=CS3)N2CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 64, 88, 88, 88, 64, 48, 44, 12, 44, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 64, 64, 64, 64, 88, 88, 48, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1] 88 rigid atoms, others: [36, 37, 38, 39, 40, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 304 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087822 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087822 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087822/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087822 Building REAL300004087823 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087823' /scratch/stefan/7774412/working/building/REAL300004087823 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087823 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087823/0 /scratch/stefan/7774412/working/building/REAL300004087823 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1042 `/scratch/stefan/7774412/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC(Cl)=C3)C=C2)S1) `REAL300004087823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087823 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC(Cl)=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 13, 13, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 5, 5, 3, 5, 5, 5, 1, 1, 6, 6, 6, 6, 11, 11, 4, 1, 1, 5, 5, 5, 5, 1, 1] 37 rigid atoms, others: [32, 33, 38, 39, 10, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087823 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC(Cl)=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 21, 21, 21, 21, 6, 6] 37 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087823 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3=CC=CC(Cl)=C3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 37, 37, 37, 21, 13, 13, 5, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 21, 37, 37, 13, 5, 5, 1, 1, 1, 1, 5, 5] 37 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 142 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087823 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087823 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087823/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087823 Building REAL300004087824 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087824' /scratch/stefan/7774412/working/building/REAL300004087824 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087824 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087824/0 /scratch/stefan/7774412/working/building/REAL300004087824 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1043 `/scratch/stefan/7774412/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3CC3(F)F)C=C2)S1) `REAL300004087824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087824 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3CC3(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 26, 38, 38, 14, 11, 11, 1, 11, 1, 1, 1, 1, 12, 12, 12, 12, 1, 1, 14, 15, 15, 15, 26, 26, 11, 12, 12, 12, 1, 1] 69 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087824 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3CC3(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 43, 43, 43, 43, 14, 14, 1, 2, 2, 2, 2, 2, 2, 43, 43, 43, 14, 14] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087824 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3CC3(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 5, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 69, 69, 69, 43, 35, 35, 12, 35, 12, 12, 1, 1, 1, 1, 1, 1, 12, 12, 43, 43, 43, 43, 69, 69, 35, 1, 1, 1, 12, 12] 69 rigid atoms, others: [14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33]) total number of confs: 247 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087824 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087824 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087824/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087824 Building REAL300004087825 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087825' /scratch/stefan/7774412/working/building/REAL300004087825 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087825 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087825/0 /scratch/stefan/7774412/working/building/REAL300004087825 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1044 `/scratch/stefan/7774412/working/3D/1044' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=C(F)C=C2)CC3)S1) `REAL300004087825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087825 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=C(F)C=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 15, 15, 15, 8, 7, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 1, 2, 3, 3, 1, 1, 8, 8, 8, 8, 15, 15, 7, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1] 15 rigid atoms, others: [32, 33, 34, 35, 40, 41, 10, 43, 12, 13, 14, 15, 16, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087825 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=C(F)C=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 9, 9, 8, 8, 9, 9, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 9, 9, 9, 9, 8, 8, 8, 8] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087825 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CC=C(F)C=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 8, 7, 3, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 9, 9, 9, 15, 15, 8, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 3] 15 rigid atoms, others: [36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 56 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087825 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087825 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087825/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087825 Building REAL300004087826 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087826' /scratch/stefan/7774412/working/building/REAL300004087826 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087826 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087826/0 /scratch/stefan/7774412/working/building/REAL300004087826 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1045 `/scratch/stefan/7774412/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1Br) `REAL300004087826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087826 none CCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 12, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 13, 25, 25, 25, 25, 25, 13, 13, 2, 2, 2, 2, 2, 2, 13] 49 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087826 none CCC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1Br NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 17, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 29, 29, 13, 13, 13, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 9, 25, 25, 13, 13, 13, 1] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 27, 28, 35] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087826 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087826 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087826/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087826 Building REAL300004087827 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087827' /scratch/stefan/7774412/working/building/REAL300004087827 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087827 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087827/0 /scratch/stefan/7774412/working/building/REAL300004087827 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1046 `/scratch/stefan/7774412/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3=CC=CC=C3)=C2)S1) `REAL300004087827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087827 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 31, 31, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 5, 5, 1, 5, 5, 1] 49 rigid atoms, others: [32, 33, 39, 10, 12, 13, 14, 15, 16, 17, 18, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087827 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 35, 35, 15, 35, 35, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 35, 35, 13, 35, 35, 13] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087827 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(=O)NC(C3=CC=CC=C3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 49, 49, 49, 35, 27, 21, 5, 21, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 35, 35, 35, 35, 49, 49, 27, 5, 5, 1, 1, 1, 1, 1, 5] 49 rigid atoms, others: [34, 35, 36, 37, 38, 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, 39]) total number of confs: 170 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087827 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087827 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087827/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087827 Building REAL300004087828 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087828' /scratch/stefan/7774412/working/building/REAL300004087828 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087828 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087828/0 /scratch/stefan/7774412/working/building/REAL300004087828 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1047 `/scratch/stefan/7774412/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)OC=C1) `REAL300004087828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087828 none COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [41, 33, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 10, 10, 41, 41, 41, 32, 32, 2, 2, 2, 2, 2, 2, 10, 10] 49 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 151 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087828 none COCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 18, 31, 31, 10, 10, 10, 1, 1, 1, 19, 19, 19, 7, 7, 5, 18, 18, 11, 11, 11, 1, 1] 49 rigid atoms, others: [32, 33, 2, 3, 4, 5, 18, 19, 20] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087828 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087828 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087828/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087828 Building REAL300004087829 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087829' /scratch/stefan/7774412/working/building/REAL300004087829 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087829 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087829/0 /scratch/stefan/7774412/working/building/REAL300004087829 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1048 `/scratch/stefan/7774412/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC(F)=CC(F)=C23)S1) `REAL300004087829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087829 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC(F)=CC(F)=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 31, 31, 31, 17, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 31, 31, 12, 1, 1, 1] 31 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 119 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087829 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=CC(F)=CC(F)=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 2, 2, 2, 2, 2, 2, 17, 17, 17] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087829 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087829 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087829/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087829 Building REAL300004087830 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087830' /scratch/stefan/7774412/working/building/REAL300004087830 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087830 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087830/0 /scratch/stefan/7774412/working/building/REAL300004087830 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1049 `/scratch/stefan/7774412/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CCCF)N=N2)S1) `REAL300004087830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087830 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CCCF)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 15, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 9, 9, 5, 5, 5, 1, 5, 1, 1, 1, 1, 7, 15, 19, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 15, 15, 19, 19] 23 rigid atoms, others: [10, 12, 13, 14, 15, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087830 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(CCCF)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 15, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 5, 5, 5, 13, 21, 23, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 13, 13, 21, 21, 23, 23] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087830 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087830 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087830/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087830 Building REAL300004087831 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087831' /scratch/stefan/7774412/working/building/REAL300004087831 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087831 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087831/0 /scratch/stefan/7774412/working/building/REAL300004087831 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1050 `/scratch/stefan/7774412/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(OC2=CN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=N2)C=N1) `REAL300004087831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087831 none CCN1C=C(OC2=CN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 35, 35, 35, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 12, 27, 27, 6, 6, 6, 1, 1, 35, 35, 74, 74, 74, 74, 74, 35, 1, 5, 12, 12, 7, 7, 7, 1, 35] 201 rigid atoms, others: [33, 5, 6, 7, 8, 9, 10, 40, 23, 24] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 350 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087831 none CCN1C=C(OC2=CN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 9, 35, 35, 35, 35, 76, 76, 76, 83, 83, 83, 120, 138, 138, 83, 83, 83, 35, 35, 1, 1, 6, 6, 6, 6, 6, 1, 35, 76, 120, 120, 83, 83, 83, 35, 1] 201 rigid atoms, others: [32, 1, 2, 3, 4, 5, 41, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087831 none CCN1C=C(OC2=CN=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 83, 83, 83, 34, 6, 6, 6, 6, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 6, 6, 83, 83, 139, 139, 139, 139, 139, 83, 6, 2, 2, 2, 2, 2, 2, 6, 83] 201 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 478 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087831 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087831 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087831/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087831 Building REAL300004087832 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087832' /scratch/stefan/7774412/working/building/REAL300004087832 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087832 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087832/0 /scratch/stefan/7774412/working/building/REAL300004087832 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1051) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1051 `/scratch/stefan/7774412/working/3D/1051' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(S2)N(C)N=C3)S1) `REAL300004087832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087832 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(S2)N(C)N=C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 13, 13, 25, 25, 25, 13, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 25, 25, 8, 1, 2, 2, 2, 1] 25 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087832 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(S2)N(C)N=C3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 8, 5, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 13, 13, 1, 2, 2, 2, 2, 2, 2, 12, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087832 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087832 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087832/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087832 Building REAL300004087833 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087833' /scratch/stefan/7774412/working/building/REAL300004087833 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087833 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087833/0 /scratch/stefan/7774412/working/building/REAL300004087833 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1052) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1052 `/scratch/stefan/7774412/working/3D/1052' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=CC=C1N1C=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087833 none COC1=CC=CC=C1N1C=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 12, 12, 16, 20, 20, 20, 33, 43, 43, 19, 19, 19, 1, 13, 13, 13, 9, 8, 9, 9, 1, 17, 33, 33, 20, 20, 20, 1] 91 rigid atoms, others: [33, 7, 8, 9, 10, 11, 12, 40, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) 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: REAL300004087833 none COC1=CC=CC=C1N1C=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 37, 37, 41, 53, 53, 53, 91, 91, 91, 53, 53, 53, 9, 4, 4, 4, 1, 1, 1, 1, 9, 41, 91, 91, 53, 53, 53, 9] 91 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 351 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087833 none COC1=CC=CC=C1N1C=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [57, 53, 53, 53, 36, 53, 53, 20, 19, 19, 19, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 19, 57, 57, 57, 53, 53, 53, 53, 20, 2, 2, 2, 2, 2, 2, 20] 91 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087833 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087833 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087833/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087833 Building REAL300004087834 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087834' /scratch/stefan/7774412/working/building/REAL300004087834 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087834 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087834/0 /scratch/stefan/7774412/working/building/REAL300004087834 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1053) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1053 `/scratch/stefan/7774412/working/3D/1053' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2)S1) `REAL300004087834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087834 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 20, 32, 32, 12, 8, 7, 1, 7, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 12, 12, 12, 12, 20, 20, 8, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 61 rigid atoms, others: [41, 10, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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: REAL300004087834 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 4, 10, 40, 40, 40, 40, 40, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 40, 40, 40, 40, 40, 40, 40, 40, 40, 12] 61 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087834 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 61, 61, 61, 40, 32, 32, 1, 32, 1, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 40, 40, 40, 61, 61, 32, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 61 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087834 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087834 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087834/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087834 Building REAL300004087835 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087835' /scratch/stefan/7774412/working/building/REAL300004087835 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087835 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087835/0 /scratch/stefan/7774412/working/building/REAL300004087835 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1054) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1054 `/scratch/stefan/7774412/working/3D/1054' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Br)=C(C)C(C)=C2)S1) `REAL300004087835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087835 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Br)=C(C)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 17, 1, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 2, 2, 2, 2, 2, 2, 1] 25 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 115 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087835 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(Br)=C(C)C(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 17, 1, 5, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087835 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087835 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087835/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087835 Building REAL300004087836 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087836' /scratch/stefan/7774412/working/building/REAL300004087836 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087836 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087836/0 /scratch/stefan/7774412/working/building/REAL300004087836 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1055) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1055 `/scratch/stefan/7774412/working/3D/1055' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3C=CCC(C3)C2)S1) `REAL300004087836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087836 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3C=CCC(C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 35 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087836 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3C=CCC(C3)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087836 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087836 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087836/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087836 Building REAL300004087837 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087837' /scratch/stefan/7774412/working/building/REAL300004087837 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087837 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087837/0 /scratch/stefan/7774412/working/building/REAL300004087837 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1056) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1056 `/scratch/stefan/7774412/working/3D/1056' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087837 none COC1=CN=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 25, 25, 25, 13, 13, 2, 2, 2, 2, 2, 2, 13] 49 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 68 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087837 none COC1=CN=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 29, 29, 13, 13, 13, 1, 3, 3, 3, 1, 1, 9, 25, 25, 13, 13, 13, 1] 49 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 20, 24, 25] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087837 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087837 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087837/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087837 Building REAL300004087838 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087838' /scratch/stefan/7774412/working/building/REAL300004087838 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087838 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087838/0 /scratch/stefan/7774412/working/building/REAL300004087838 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1057) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1057 `/scratch/stefan/7774412/working/3D/1057' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=CC=C3)C(CC(C)C)=C2)S1) `REAL300004087838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087838 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=CC=C3)C(CC(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 24, 24, 8, 5, 5, 1, 5, 1, 1, 1, 1, 4, 4, 2, 4, 4, 1, 1, 4, 4, 4, 1, 8, 8, 8, 8, 14, 14, 5, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 46 rigid atoms, others: [10, 12, 13, 14, 15, 48, 21, 22, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 113 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087838 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=CC=C3)C(CC(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 8, 8, 8, 16, 16, 13, 16, 16, 8, 8, 18, 18, 18, 8, 1, 2, 2, 2, 2, 2, 2, 16, 16, 14, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8] 46 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 27] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 112 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087838 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN(C3=CC=CC=C3)C(CC(C)C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 30, 36, 36, 16, 10, 10, 4, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 4, 16, 16, 16, 16, 30, 30, 10, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4] 46 rigid atoms, others: [34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087838 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087838 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087838/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087838 Building REAL300004087839 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087839' /scratch/stefan/7774412/working/building/REAL300004087839 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087839 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087839/0 /scratch/stefan/7774412/working/building/REAL300004087839 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1058) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1058 `/scratch/stefan/7774412/working/3D/1058' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)CC3)C=C2)S1) `REAL300004087839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087839 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 23, 23, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 33 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 46, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087839 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 3, 3, 24, 24, 24, 24, 24, 24, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 24, 24, 24, 24, 24, 24, 24, 23, 24, 24, 24, 24, 7, 7] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087839 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(N3CCC(C)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 33, 33, 33, 24, 19, 18, 1, 18, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 33, 33, 19, 9, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 9, 9] 33 rigid atoms, others: [34, 35, 36, 37, 38, 44, 43, 45, 15, 16, 17, 18, 19, 20, 21, 22, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087839 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087839 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087839/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087839 Building REAL300004087840 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087840' /scratch/stefan/7774412/working/building/REAL300004087840 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087840 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087840/0 /scratch/stefan/7774412/working/building/REAL300004087840 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1059) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1059 `/scratch/stefan/7774412/working/3D/1059' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1) `REAL300004087840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087840 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 33, 50, 50, 17, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 17, 17, 17, 17, 33, 33, 12, 1, 1, 1, 1, 10, 10, 10, 10, 10] 82 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087840 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 17, 17, 17, 17, 17, 17, 17, 68, 68, 68, 68, 68, 1, 2, 2, 2, 2, 2, 3, 17, 17, 17, 17, 68, 68, 68, 68, 68] 82 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087840 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 82, 82, 82, 68, 53, 48, 10, 48, 10, 10, 10, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 82, 82, 53, 10, 10, 10, 10, 1, 1, 2, 2, 2] 82 rigid atoms, others: [36, 37, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 253 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087840 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087840/1 /scratch/stefan/7774412/working/building/REAL300004087840 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1060) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1060 `/scratch/stefan/7774412/working/3D/1060' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1) `REAL300004087840.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087840 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 27, 28, 28, 23, 15, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 23, 23, 23, 23, 27, 27, 1, 1, 1, 1, 6, 6, 6, 6, 6] 28 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087840 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 18, 18, 23, 23, 23, 23, 23, 23, 23, 26, 26, 26, 26, 26, 1, 2, 2, 2, 2, 2, 23, 23, 23, 23, 26, 26, 26, 26, 26] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087840 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=NC=CN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 8, 1, 1, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 28, 28, 28, 26, 19, 12, 6, 12, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 28, 28, 6, 6, 6, 6, 1, 1, 2, 2, 2] 28 rigid atoms, others: [35, 36, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39]) total number of confs: 74 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087840 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087840 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087840/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087840/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087840 Building REAL300004087841 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087841' /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for REAL300004087841 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087841/0 /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1061) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1061 `/scratch/stefan/7774412/working/3D/1061' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](C(C)C)C2)S1) `REAL300004087841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 5, 6, 6, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1] 10 rigid atoms, others: [32, 33, 34, 35, 44, 10, 43, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 31 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 8, 8, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 4, 4] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087841/1 /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1062) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1062 `/scratch/stefan/7774412/working/3D/1062' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](C(C)C)C2)S1) `REAL300004087841.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087841/1/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: REAL300004087841 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 5, 6, 6, 4, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 4, 4, 4, 4, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 1, 1] 10 rigid atoms, others: [32, 33, 34, 35, 44, 10, 43, 12, 13, 14, 15, 16, 17, 18, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 40 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC[N@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 8, 8, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 4, 4] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 54 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087841/2 /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 1063) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1063 `/scratch/stefan/7774412/working/3D/1063' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+](C(C)C)C2)S1) `REAL300004087841.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087841/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 7, 7, 6, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 1, 1] 8 rigid atoms, others: [32, 33, 34, 10, 43, 12, 13, 14, 15, 16, 17, 18, 42, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 29 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 6, 6] 8 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `3' /scratch/stefan/7774412/working/building/REAL300004087841/3 /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 3 (index: 1064) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1064 `/scratch/stefan/7774412/working/3D/1064' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+](C(C)C)C2)S1) `REAL300004087841.mol2' -> `3.mol2' `temp.mol2' -> `REAL300004087841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087841/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 8, 8, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 1, 1] 8 rigid atoms, others: [32, 33, 34, 10, 43, 12, 13, 14, 15, 16, 17, 18, 42, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 46 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087841 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCC[N@H+](C(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 1, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 6, 6] 8 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087841 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087841 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087841/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087841/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087841/0.* 3: /scratch/stefan/7774412/working/building/REAL300004087841/3.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087841 Building REAL300004087842 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087842' /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004087842 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087842/0 /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1065) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1065 `/scratch/stefan/7774412/working/3D/1065' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](C)CC2C(F)(F)F)S1) `REAL300004087842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087842 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](C)CC2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 8, 8, 8, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 8, 8, 5, 1, 1, 1, 2, 2, 2, 1, 1, 1] 8 rigid atoms, others: [32, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087842 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@@H+](C)CC2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5] 8 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087842/1 /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1066) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1066 `/scratch/stefan/7774412/working/3D/1066' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](C)CC2C(F)(F)F)S1) `REAL300004087842.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087842/1/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: REAL300004087842 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](C)CC2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1] 2 rigid atoms, others: [32, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087842 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C[N@H+](C)CC2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 17 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `2' /scratch/stefan/7774412/working/building/REAL300004087842/2 /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 2 (index: 1067) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1067 `/scratch/stefan/7774412/working/3D/1067' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CN(C)CC2C(F)(F)F)S1) `REAL300004087842.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004087842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087842/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087842 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CN(C)CC2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 8, 8, 8, 5, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 8, 8, 4, 1, 1, 1, 2, 2, 2, 1, 1, 1] 8 rigid atoms, others: [35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087842 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CN(C)CC2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 10, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 8 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087842 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087842 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 2: /scratch/stefan/7774412/working/building/REAL300004087842/2.* 1: /scratch/stefan/7774412/working/building/REAL300004087842/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087842/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087842 Building REAL300004087843 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087843' /scratch/stefan/7774412/working/building/REAL300004087843 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087843 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087843/0 /scratch/stefan/7774412/working/building/REAL300004087843 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1068) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1068 `/scratch/stefan/7774412/working/3D/1068' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1F) `REAL300004087843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087843 none COC1=CC=C(C(C)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 88, 88, 88, 88, 22, 3, 22, 2, 3, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 88, 88, 88, 133, 133, 133, 88, 88, 22, 22, 22, 22, 2, 3, 3, 2, 2, 2, 88] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 274 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087843 none COC1=CC=C(C(C)C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 12, 12, 63, 63, 72, 88, 88, 88, 156, 201, 201, 88, 88, 88, 1, 1, 1, 4, 4, 4, 1, 1, 12, 12, 12, 12, 72, 156, 156, 89, 89, 89, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 831 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087843 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087843/1 /scratch/stefan/7774412/working/building/REAL300004087843 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1069) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1069 `/scratch/stefan/7774412/working/3D/1069' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1F) `REAL300004087843.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087843/1/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: REAL300004087843 none COC1=CC=C(C(C)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [169, 136, 136, 136, 136, 73, 41, 73, 12, 41, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 136, 136, 136, 169, 169, 169, 136, 136, 73, 73, 73, 73, 2, 2, 2, 2, 2, 136] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087843 none COC1=CC=C(C(C)C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 60, 136, 136, 136, 192, 201, 201, 136, 136, 136, 1, 1, 1, 3, 3, 3, 1, 1, 4, 5, 5, 5, 192, 192, 136, 136, 136, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 21, 22, 23, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 595 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087843 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087843 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087843/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087843/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087843 Building REAL300004087844 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087844' /scratch/stefan/7774412/working/building/REAL300004087844 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087844 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087844/0 /scratch/stefan/7774412/working/building/REAL300004087844 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1070) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1070 `/scratch/stefan/7774412/working/3D/1070' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CC(F)(F)C1) `REAL300004087844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087844 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 1, 6, 16, 16, 16, 24, 24, 24, 39, 39, 39, 24, 24, 24, 1, 1, 1, 1, 1, 1, 11, 11, 11, 6, 16, 39, 39, 24, 24, 24, 1, 1, 1, 1, 1] 39 rigid atoms, others: [32, 33, 2, 35, 36, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 159 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087844 none COC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 24, 24, 24, 24, 24, 19, 19, 19, 14, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24] 39 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087844 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087844/1 /scratch/stefan/7774412/working/building/REAL300004087844 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1071) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1071 `/scratch/stefan/7774412/working/3D/1071' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1CC(F)(F)C1) `REAL300004087844.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087844/1/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: REAL300004087844 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 1, 8, 25, 25, 59, 153, 153, 153, 199, 201, 201, 153, 153, 153, 1, 1, 1, 1, 1, 1, 15, 15, 15, 8, 199, 199, 153, 153, 153, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 34, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087844 none COC(C(=O)[N-]C1=NC(CC(=O)[O-])=C(C)S1)C1CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 94, 49, 13, 49, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 94, 153, 153, 153, 153, 153, 106, 106, 106, 94, 2, 2, 2, 2, 2, 153, 153, 153, 153, 153] 201 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 599 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087844 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087844 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087844/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087844/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087844 Building REAL300004087845 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087845' /scratch/stefan/7774412/working/building/REAL300004087845 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087845 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087845/0 /scratch/stefan/7774412/working/building/REAL300004087845 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1072) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1072 `/scratch/stefan/7774412/working/3D/1072' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCCOC2)S1) `REAL300004087845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087845 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCCOC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 12, 12, 12, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087845 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2CCCOC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 6, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10] 12 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087845 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087845/1 /scratch/stefan/7774412/working/building/REAL300004087845 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1073) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1073 `/scratch/stefan/7774412/working/3D/1073' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCCOC2)S1) `REAL300004087845.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087845/1/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: REAL300004087845 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCCOC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 201, 201, 201, 176, 103, 58, 22, 58, 8, 1, 1, 1, 1, 1, 1, 1, 176, 176, 176, 176, 201, 201, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 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: REAL300004087845 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2CCCOC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 36, 36, 80, 151, 176, 176, 176, 176, 176, 1, 2, 2, 2, 3, 3, 80, 80, 176, 176, 176, 176, 176, 176, 176, 176, 176] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087845 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087845 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087845/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087845/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087845 Building REAL300004087846 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087846' /scratch/stefan/7774412/working/building/REAL300004087846 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087846 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087846/0 /scratch/stefan/7774412/working/building/REAL300004087846 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1074) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1074 `/scratch/stefan/7774412/working/3D/1074' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC(C3CC3)=NO2)S1) `REAL300004087846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087846 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC(C3CC3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 130, 159, 159, 116, 116, 116, 116, 116, 39, 9, 1, 1, 1, 1, 1, 12, 12, 1, 1, 116, 116, 116, 116, 130, 130, 116, 116, 116, 9, 9, 12, 12, 12, 12, 12] 201 rigid atoms, others: [14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 621 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087846 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC(C3CC3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 2, 6, 24, 116, 116, 116, 194, 194, 116, 116, 1, 2, 2, 2, 2, 2, 2, 2, 2, 24, 24, 194, 194, 194, 194, 194] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087846 none CC1=C(CC(=O)[O-])N=C(NC(=O)COCC2=NC(C3CC3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 194, 201, 201, 201, 194, 194, 194, 194, 194, 160, 77, 12, 12, 12, 1, 1, 1, 1, 12, 12, 194, 194, 194, 194, 201, 201, 194, 194, 194, 77, 77, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 592 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087846 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087846/1 /scratch/stefan/7774412/working/building/REAL300004087846 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1075) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1075 `/scratch/stefan/7774412/working/3D/1075' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC(C3CC3)=NO2)S1) `REAL300004087846.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087846/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087846 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC(C3CC3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 109, 111, 111, 106, 70, 63, 22, 63, 5, 5, 1, 1, 1, 1, 1, 7, 7, 1, 1, 106, 106, 106, 106, 109, 109, 22, 22, 5, 5, 7, 7, 7, 7, 7] 166 rigid atoms, others: [14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087846 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC(C3CC3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 18, 18, 26, 34, 34, 106, 106, 106, 164, 164, 106, 106, 1, 2, 2, 2, 2, 2, 26, 26, 34, 34, 164, 164, 164, 164, 164] 166 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 452 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087846 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COCC2=NC(C3CC3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 1, 8, 1, 5, 5, 5, 8, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 166, 166, 166, 164, 127, 120, 58, 120, 21, 21, 7, 7, 7, 1, 1, 1, 1, 7, 7, 164, 164, 164, 164, 166, 166, 58, 58, 21, 21, 1, 1, 1, 1, 1] 166 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 506 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087846 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087846 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087846/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087846/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087846 Building REAL300004087847 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087847' /scratch/stefan/7774412/working/building/REAL300004087847 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087847 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087847/0 /scratch/stefan/7774412/working/building/REAL300004087847 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1076) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1076 `/scratch/stefan/7774412/working/3D/1076' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C3C(=C2)CCN3C)S1) `REAL300004087847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087847 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C3C(=C2)CCN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 71, 71, 71, 37, 21, 21, 6, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 71, 71, 21, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 71 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41]) total number of confs: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087847 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2=CC=C3C(=C2)CCN3C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 33, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 2, 2, 3, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37] 71 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087847 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087847 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087847/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087847 Building REAL300004087848 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087848' /scratch/stefan/7774412/working/building/REAL300004087848 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087848 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087848/0 /scratch/stefan/7774412/working/building/REAL300004087848 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1077) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1077 `/scratch/stefan/7774412/working/3D/1077' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C(C)(C)C)C2)S1) `REAL300004087848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087848 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C(C)(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1] 25 rigid atoms, others: [44, 10, 43, 12, 13, 14, 15, 16, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 111 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087848 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C(C)(C)C)C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 3, 3, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087848 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087848 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087848/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087848 Building REAL300004087849 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087849' /scratch/stefan/7774412/working/building/REAL300004087849 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087849 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087849/0 /scratch/stefan/7774412/working/building/REAL300004087849 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1078) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1078 `/scratch/stefan/7774412/working/3D/1078' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C) `REAL300004087849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087849 none CC1=CC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 15, 10, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 15, 15, 10, 10, 2, 2, 2, 2, 2, 2, 30, 30, 30] 54 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087849 none CC1=CC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 15, 30, 30, 30, 30, 30, 30, 54, 54, 54, 30, 30, 30, 1, 1, 1, 2, 2, 2, 1, 7, 7, 15, 15, 30, 54, 54, 30, 30, 30, 2, 2, 2] 54 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 21, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 262 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087849 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087849 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087849/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087849 Building REAL300004087850 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087850' /scratch/stefan/7774412/working/building/REAL300004087850 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087850 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087850/0 /scratch/stefan/7774412/working/building/REAL300004087850 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1079) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1079 `/scratch/stefan/7774412/working/3D/1079' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)NC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087850 none CCS(=O)(=O)NC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [48, 41, 25, 41, 41, 9, 5, 9, 9, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 9, 48, 48, 48, 48, 48, 25, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9] 78 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087850 none CCS(=O)(=O)NC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 8, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [22, 14, 6, 14, 14, 1, 1, 1, 1, 1, 1, 7, 7, 7, 9, 9, 9, 17, 32, 32, 9, 9, 9, 1, 1, 22, 22, 22, 22, 22, 6, 1, 1, 7, 17, 17, 9, 9, 9, 1, 1] 78 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 39, 40, 23, 24, 31] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087850 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087850 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087850/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087850 Building REAL300004087851 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087851' /scratch/stefan/7774412/working/building/REAL300004087851 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087851 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087851/0 /scratch/stefan/7774412/working/building/REAL300004087851 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1080) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1080 `/scratch/stefan/7774412/working/3D/1080' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087851 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 49, 49, 49, 31, 23, 21, 7, 21, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 31, 31, 49, 49, 23, 7, 21, 1, 1, 1, 1] 147 rigid atoms, others: [33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 217 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087851 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 3, 3, 22, 23, 31, 31, 25, 30, 31, 31, 31, 31, 31, 1, 2, 2, 2, 3, 3, 2, 23, 69, 31, 31, 31, 31] 147 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087851 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087851/1 /scratch/stefan/7774412/working/building/REAL300004087851 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1081) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1081 `/scratch/stefan/7774412/working/3D/1081' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087851.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087851/1/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: REAL300004087851 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 201, 201, 201, 161, 75, 30, 7, 30, 1, 7, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 161, 161, 161, 161, 201, 201, 7, 21, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 543 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087851 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 42, 42, 119, 119, 161, 161, 141, 146, 161, 161, 161, 161, 161, 1, 2, 2, 2, 2, 2, 119, 357, 161, 161, 161, 161] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1043 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087851 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087851 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087851/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087851/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087851 Building REAL300004087852 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087852' /scratch/stefan/7774412/working/building/REAL300004087852 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087852 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087852/0 /scratch/stefan/7774412/working/building/REAL300004087852 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1082) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1082 `/scratch/stefan/7774412/working/3D/1082' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC=C2C(F)(F)F)S1) `REAL300004087852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087852 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 52, 52, 52, 31, 28, 23, 6, 23, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 31, 31, 31, 31, 52, 52, 28, 6, 18, 1, 1, 1, 1] 156 rigid atoms, others: [33, 34, 35, 36, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087852 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=CC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 156 conformations in input total number of sets (complete confs): 156 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 18, 19, 31, 31, 22, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 2, 2, 2, 19, 57, 31, 31, 24, 31] 156 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087852 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087852/1 /scratch/stefan/7774412/working/building/REAL300004087852 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1083) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1083 `/scratch/stefan/7774412/working/3D/1083' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC=C2C(F)(F)F)S1) `REAL300004087852.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087852/1/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: REAL300004087852 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 201, 201, 201, 136, 48, 16, 6, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 136, 136, 136, 136, 201, 201, 6, 18, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087852 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=CC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 68, 68, 122, 122, 136, 136, 126, 136, 136, 136, 136, 136, 136, 1, 2, 2, 2, 3, 3, 122, 366, 136, 136, 126, 136] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 864 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087852 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087852 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087852/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087852/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087852 Building REAL300004087853 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087853' /scratch/stefan/7774412/working/building/REAL300004087853 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087853 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087853/0 /scratch/stefan/7774412/working/building/REAL300004087853 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1084) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1084 `/scratch/stefan/7774412/working/3D/1084' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(Cl)C(Cl)=C2)S1) `REAL300004087853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087853 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(Cl)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 67, 67, 67, 43, 40, 40, 11, 40, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 67, 67, 40, 11, 33, 1, 1, 1] 201 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 293 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087853 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC=C(Cl)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 3, 3, 15, 15, 43, 43, 41, 43, 43, 43, 43, 1, 2, 2, 2, 3, 3, 2, 15, 45, 43, 43, 43] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087853 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087853/1 /scratch/stefan/7774412/working/building/REAL300004087853 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1085) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1085 `/scratch/stefan/7774412/working/3D/1085' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(Cl)C(Cl)=C2)S1) `REAL300004087853.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087853/1/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: REAL300004087853 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(Cl)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 201, 201, 201, 166, 88, 40, 11, 40, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 201, 201, 11, 33, 1, 1, 1] 603 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 550 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087853 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC=C(Cl)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 36, 36, 84, 84, 166, 166, 149, 166, 166, 166, 166, 1, 2, 2, 2, 2, 2, 84, 252, 166, 166, 166] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087853 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087853 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087853/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087853/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087853 Building REAL300004087854 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087854' /scratch/stefan/7774412/working/building/REAL300004087854 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087854 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087854/0 /scratch/stefan/7774412/working/building/REAL300004087854 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1086) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1086 `/scratch/stefan/7774412/working/3D/1086' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C(F)F)S1) `REAL300004087854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087854 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 16, 25, 29, 29, 15, 13, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 16, 16, 16, 25, 25, 13, 1, 1, 1, 1, 9] 33 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087854 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 5, 15, 15, 16, 25, 25, 1, 2, 2, 2, 2, 2, 2, 15, 15, 5, 15, 25] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087854 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087854 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087854/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087854 Building REAL300004087855 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087855' /scratch/stefan/7774412/working/building/REAL300004087855 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087855 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087855/0 /scratch/stefan/7774412/working/building/REAL300004087855 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1087) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1087 `/scratch/stefan/7774412/working/3D/1087' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CN=C3)=NO2)S1) `REAL300004087855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087855 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CN=C3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 25, 45, 57, 57, 24, 16, 12, 1, 12, 1, 1, 1, 1, 12, 12, 12, 12, 12, 1, 1, 24, 25, 25, 25, 45, 45, 16, 1, 13, 13, 12, 13] 104 rigid atoms, others: [10, 12, 13, 14, 15, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087855 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CN=C3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 24, 58, 58, 58, 58, 58, 24, 24, 1, 2, 2, 2, 2, 2, 2, 24, 58, 59, 58, 58] 104 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087855 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3=CC=CN=C3)=NO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 1, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 104, 104, 104, 59, 49, 44, 13, 45, 12, 12, 1, 1, 1, 1, 1, 1, 1, 12, 12, 59, 59, 59, 59, 104, 104, 48, 13, 1, 1, 1, 1] 104 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 413 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087855 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087855 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087855/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087855 Building REAL300004087856 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087856' /scratch/stefan/7774412/working/building/REAL300004087856 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087856 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087856/0 /scratch/stefan/7774412/working/building/REAL300004087856 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1088) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1088 `/scratch/stefan/7774412/working/3D/1088' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2CCCCCC2)S1) `REAL300004087856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087856 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 61, 61, 61, 34, 29, 25, 6, 25, 1, 6, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 61, 61, 29, 6, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 183 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 273 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087856 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 17, 34, 34, 34, 34, 34, 34, 1, 2, 2, 2, 2, 2, 2, 17, 51, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 183 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 190 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087856 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087856/1 /scratch/stefan/7774412/working/building/REAL300004087856 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1089) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1089 `/scratch/stefan/7774412/working/3D/1089' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2CCCCCC2)S1) `REAL300004087856.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087856/1/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: REAL300004087856 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 201, 201, 201, 156, 65, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 201, 201, 7, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 549 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087856 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2CCCCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 40, 40, 103, 103, 156, 156, 156, 156, 156, 156, 1, 2, 2, 2, 2, 2, 103, 309, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156, 156] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 883 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087856 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087856 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087856/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087856/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087856 Building REAL300004087857 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087857' /scratch/stefan/7774412/working/building/REAL300004087857 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087857 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087857/0 /scratch/stefan/7774412/working/building/REAL300004087857 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1090) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1090 `/scratch/stefan/7774412/working/3D/1090' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1CC) `REAL300004087857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087857 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 22, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 22, 22, 22, 22, 64, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 22, 64, 64, 64, 64, 64] 103 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087857 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=NN1CC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 9, 9, 13, 22, 22, 22, 39, 57, 57, 22, 22, 22, 1, 1, 1, 1, 5, 5, 5, 5, 4, 4, 13, 39, 39, 22, 22, 22, 1, 5, 5, 5, 5, 5] 103 rigid atoms, others: [1, 2, 3, 4, 33, 17, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087857 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087857 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087857/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087857 Building REAL300004087858 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087858' /scratch/stefan/7774412/working/building/REAL300004087858 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087858 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087858/0 /scratch/stefan/7774412/working/building/REAL300004087858 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1091) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1091 `/scratch/stefan/7774412/working/3D/1091' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC(F)=CC(F)=C2)S1) `REAL300004087858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087858 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 40, 40, 40, 29, 26, 26, 7, 26, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 40, 40, 26, 7, 21, 1, 1, 1] 120 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 165 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087858 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(O)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 6, 6, 1, 1, 1, 2, 3, 3, 15, 16, 27, 27, 27, 16, 27, 27, 27, 1, 2, 2, 2, 3, 3, 2, 16, 48, 27, 16, 27] 120 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087858 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087858/1 /scratch/stefan/7774412/working/building/REAL300004087858 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1092) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1092 `/scratch/stefan/7774412/working/3D/1092' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC(F)=CC(F)=C2)S1) `REAL300004087858.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087858/1/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: REAL300004087858 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 172, 172, 201, 201, 201, 172, 78, 33, 10, 33, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 201, 201, 10, 30, 1, 1, 1] 603 rigid atoms, others: [32, 12, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087858 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(O)C2=CC(F)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 42, 42, 113, 113, 168, 168, 168, 113, 168, 168, 168, 1, 2, 2, 2, 2, 2, 113, 339, 168, 113, 168] 603 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 997 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087858 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087858 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087858/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087858/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087858 Building REAL300004087859 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087859' /scratch/stefan/7774412/working/building/REAL300004087859 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087859 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087859/0 /scratch/stefan/7774412/working/building/REAL300004087859 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1093) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1093 `/scratch/stefan/7774412/working/3D/1093' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=CC=C2)C(F)F)S1) `REAL300004087859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087859 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=CC=C2)C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 14, 18, 18, 9, 9, 8, 7, 8, 3, 1, 1, 1, 1, 1, 1, 1, 3, 11, 11, 9, 9, 9, 9, 14, 14, 9, 7, 7, 3, 1, 1, 1, 1, 1, 11] 18 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087859 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=CC=C2)C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 3, 7, 9, 9, 7, 9, 9, 7, 15, 15, 1, 2, 2, 2, 2, 2, 2, 3, 3, 7, 9, 9, 7, 9, 9, 15] 18 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087859 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087859 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087859/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087859 Building REAL300004087860 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087860' /scratch/stefan/7774412/working/building/REAL300004087860 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087860 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087860/0 /scratch/stefan/7774412/working/building/REAL300004087860 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1094) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1094 `/scratch/stefan/7774412/working/3D/1094' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCOCC3=C2)S1) `REAL300004087860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087860 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCOCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087860 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCOCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087860 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087860 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087860/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087860 Building REAL300004087861 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087861' /scratch/stefan/7774412/working/building/REAL300004087861 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087861 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087861/0 /scratch/stefan/7774412/working/building/REAL300004087861 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1095) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1095 `/scratch/stefan/7774412/working/3D/1095' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1) `REAL300004087861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087861 none CCOCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [131, 125, 65, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 131, 131, 131, 131, 131, 64, 64, 2, 2, 2, 2, 2, 2, 14] 192 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 373 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: REAL300004087861 none CCOCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [61, 42, 8, 1, 1, 1, 1, 1, 10, 10, 10, 14, 14, 14, 27, 53, 53, 13, 13, 13, 1, 1, 61, 61, 61, 60, 60, 8, 8, 10, 27, 27, 14, 14, 14, 1] 192 rigid atoms, others: [3, 4, 5, 6, 7, 35, 20, 21] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 366 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087861 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087861 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087861/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087861 Building REAL300004087862 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087862' /scratch/stefan/7774412/working/building/REAL300004087862 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087862 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087862/0 /scratch/stefan/7774412/working/building/REAL300004087862 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1096) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1096 `/scratch/stefan/7774412/working/3D/1096' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C3CCOC3)N=N2)S1) `REAL300004087862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087862 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C3CCOC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 12, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 7, 7, 11, 15, 15, 6, 5, 5, 1, 5, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 6, 7, 7, 7, 11, 11, 5, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6] 19 rigid atoms, others: [10, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087862 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C3CCOC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 12, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 6, 7, 6, 7, 11, 11, 11, 11, 6, 6, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087862 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N(C3CCOC3)N=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 5, 5, 5, 12, 5, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 19, 19, 19, 11, 9, 9, 6, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 19, 19, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087862 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087862 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087862/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087862 Building REAL300004087863 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087863' /scratch/stefan/7774412/working/building/REAL300004087863 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087863 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087863/0 /scratch/stefan/7774412/working/building/REAL300004087863 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1097) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1097 `/scratch/stefan/7774412/working/3D/1097' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N1C) `REAL300004087863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087863 none CC1=NN=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 12, 10, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 17, 17, 17, 17, 17, 12, 12, 10, 10, 2, 2, 2, 2, 2, 2, 17, 17, 17] 19 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087863 none CC1=NN=C(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 10, 14, 14, 15, 17, 17, 17, 19, 19, 19, 17, 17, 17, 1, 1, 2, 2, 2, 4, 4, 10, 10, 15, 19, 19, 17, 17, 17, 2, 2, 2] 19 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087863 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087863 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087863/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087863 Building REAL300004087864 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087864' /scratch/stefan/7774412/working/building/REAL300004087864 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087864 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087864/0 /scratch/stefan/7774412/working/building/REAL300004087864 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1098) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1098 `/scratch/stefan/7774412/working/3D/1098' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NN=NN3C2)S1) `REAL300004087864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087864 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NN=NN3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 12, 23, 23, 23, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 12, 12, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087864 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NN=NN3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 8, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 11, 11, 11, 11, 12, 12, 12, 11, 1, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087864 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087864 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087864/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087864 Building REAL300004087865 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087865' /scratch/stefan/7774412/working/building/REAL300004087865 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087865 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087865/0 /scratch/stefan/7774412/working/building/REAL300004087865 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1099) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1099 `/scratch/stefan/7774412/working/3D/1099' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=C(Cl)C=C3N2)S1) `REAL300004087865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087865 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=C(Cl)C=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 16, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 14, 26, 26, 26, 13, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 14, 14, 14, 26, 26, 9, 1, 2, 2, 2, 1, 1, 1] 26 rigid atoms, others: [34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 23, 24, 25, 26, 27, 28, 29, 31]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087865 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C)C=C(Cl)C=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 16, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 14, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 13, 13] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087865 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087865 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087865/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087865 Building REAL300004087866 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087866' /scratch/stefan/7774412/working/building/REAL300004087866 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087866 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087866/0 /scratch/stefan/7774412/working/building/REAL300004087866 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1100) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1100 `/scratch/stefan/7774412/working/3D/1100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1) `REAL300004087866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087866 none CC1=C(C)NC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 6, 4, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 4, 4, 2, 3, 3, 2, 2, 2] 13 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087866 none CC1=C(C)NC(CCC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 9, 11, 11, 11, 11, 11, 11, 13, 13, 13, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 1, 7, 7, 9, 9, 11, 13, 13, 11, 11, 11] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087866 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087866 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087866/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087866 Building REAL300004087867 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087867' /scratch/stefan/7774412/working/building/REAL300004087867 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087867 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087867/0 /scratch/stefan/7774412/working/building/REAL300004087867 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1101) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1101 `/scratch/stefan/7774412/working/3D/1101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1) `REAL300004087867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087867 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 40, 61, 61, 21, 11, 11, 1, 11, 1, 1, 6, 6, 6, 3, 6, 6, 6, 1, 1, 1, 21, 22, 22, 22, 40, 40, 11, 6, 5, 6, 1, 1, 1, 1, 1, 1] 90 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 258 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087867 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 21, 50, 50, 50, 43, 50, 50, 50, 21, 21, 21, 1, 2, 2, 2, 2, 2, 2, 50, 50, 50, 21, 21, 22, 22, 21, 22] 90 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087867 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 90, 90, 90, 50, 33, 33, 6, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 90, 90, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6] 90 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 351 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087867 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087867/1 /scratch/stefan/7774412/working/building/REAL300004087867 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1102) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1102 `/scratch/stefan/7774412/working/3D/1102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1) `REAL300004087867.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087867 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 123, 123, 123, 156, 163, 163, 123, 47, 10, 1, 10, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 123, 123, 123, 123, 156, 156, 3, 3, 3, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 10, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 403 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087867 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 12, 39, 39, 123, 163, 163, 163, 163, 163, 163, 163, 123, 123, 123, 1, 2, 2, 2, 2, 2, 163, 163, 163, 123, 123, 123, 123, 123, 123] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087867 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(Cl)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 16, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 74, 20, 3, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 163, 163, 163, 163, 201, 201, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 477 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087867 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087867 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087867/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087867/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087867 Building REAL300004087868 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087868' /scratch/stefan/7774412/working/building/REAL300004087868 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087868 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087868/0 /scratch/stefan/7774412/working/building/REAL300004087868 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1103) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1103 `/scratch/stefan/7774412/working/3D/1103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1) `REAL300004087868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087868 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 21, 40, 64, 64, 21, 11, 11, 1, 11, 1, 1, 6, 6, 6, 5, 6, 6, 6, 1, 1, 1, 21, 22, 22, 22, 40, 40, 11, 6, 5, 6, 1, 1, 1, 1, 1, 1] 88 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 262 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087868 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 21, 51, 51, 51, 51, 51, 51, 51, 21, 21, 21, 1, 2, 2, 2, 2, 2, 2, 51, 51, 51, 21, 21, 22, 22, 21, 22] 88 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 128 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087868 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 88, 88, 88, 51, 33, 33, 6, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 51, 51, 51, 51, 88, 88, 33, 1, 1, 1, 6, 6, 6, 6, 6, 6] 88 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 335 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087868 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087868/1 /scratch/stefan/7774412/working/building/REAL300004087868 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1104) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1104 `/scratch/stefan/7774412/working/3D/1104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1) `REAL300004087868.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087868/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087868 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 125, 125, 125, 153, 159, 159, 125, 51, 10, 1, 10, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 125, 125, 125, 125, 153, 153, 3, 3, 3, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 10, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087868 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 36, 36, 125, 163, 163, 163, 163, 163, 163, 163, 125, 125, 125, 1, 2, 2, 2, 2, 2, 163, 163, 163, 125, 125, 125, 125, 125, 125] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087868 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=CC(F)=CC=C3F)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 1, 15, 1, 1, 1, 15, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 81, 21, 3, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 163, 163, 163, 163, 201, 201, 1, 1, 1, 3, 3, 3, 3, 3, 3] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 478 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087868 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087868 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087868/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087868/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087868 Building REAL300004087869 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087869' /scratch/stefan/7774412/working/building/REAL300004087869 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087869 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087869/0 /scratch/stefan/7774412/working/building/REAL300004087869 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1105) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1105 `/scratch/stefan/7774412/working/3D/1105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2CC2)S1) `REAL300004087869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087869 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 3, 2, 2, 3, 3, 3, 3, 3] 9 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087869 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5] 9 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087869 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2N=NN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 9, 9, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1] 9 rigid atoms, others: [32, 33, 34, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 40 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087869 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087869/1 /scratch/stefan/7774412/working/building/REAL300004087869 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1106) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1106 `/scratch/stefan/7774412/working/3D/1106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2CC2)S1) `REAL300004087869.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087869 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [105, 105, 105, 105, 140, 163, 163, 105, 48, 20, 6, 20, 1, 1, 1, 1, 1, 1, 1, 7, 7, 105, 105, 105, 105, 140, 140, 6, 6, 7, 7, 7, 7, 7] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087869 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 29, 29, 72, 105, 105, 105, 105, 105, 165, 165, 1, 2, 2, 2, 2, 2, 72, 72, 165, 165, 165, 165, 165] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 547 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087869 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2N=NN=C2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 8, 8, 8, 1, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [165, 165, 165, 165, 201, 201, 201, 165, 106, 70, 27, 70, 7, 7, 7, 7, 7, 1, 1, 1, 1, 165, 165, 165, 165, 201, 201, 27, 27, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 582 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087869 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087869 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087869/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087869/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087869 Building REAL300004087870 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087870' /scratch/stefan/7774412/working/building/REAL300004087870 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087870 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087870/0 /scratch/stefan/7774412/working/building/REAL300004087870 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1107) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1107 `/scratch/stefan/7774412/working/3D/1107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(N3C=NN=N3)CCSCC2)S1) `REAL300004087870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087870 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(N3C=NN=N3)CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 14, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087870 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(N3C=NN=N3)CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 14, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 2, 4, 7, 7, 7, 7, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 4, 4, 4, 4, 4, 4, 4, 4] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087870 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2(N3C=NN=N3)CCSCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 8, 8, 8, 5, 5, 14, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 7, 7, 13, 13, 7, 7, 7, 1, 3, 3, 3, 3, 3, 3, 3, 3] 13 rigid atoms, others: [33, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087870 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087870 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087870/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087870 Building REAL300004087871 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087871' /scratch/stefan/7774412/working/building/REAL300004087871 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087871 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087871/0 /scratch/stefan/7774412/working/building/REAL300004087871 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1108) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1108 `/scratch/stefan/7774412/working/3D/1108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(N)=O)C(Cl)=C2)S1) `REAL300004087871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087871 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(N)=O)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 5, 5, 5, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 5, 5, 3, 1, 1, 3, 3, 1] 5 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 31, 32]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087871 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(N)=O)C(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3] 5 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 23 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087871 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087871 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087871/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087871 Building REAL300004087872 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087872' /scratch/stefan/7774412/working/building/REAL300004087872 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087872 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087872/0 /scratch/stefan/7774412/working/building/REAL300004087872 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1109) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1109 `/scratch/stefan/7774412/working/3D/1109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC3=CC=CC=C3N=C2)S1) `REAL300004087872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087872 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC3=CC=CC=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [34, 34, 34, 34, 52, 53, 53, 34, 31, 25, 11, 31, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 35, 35, 35, 52, 52, 25, 11, 11, 1, 1, 1, 1, 1] 53 rigid atoms, others: [33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 211 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087872 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=NC3=CC=CC=C3N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 16, 16, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 2, 2, 2, 2, 2, 2, 16, 16, 34, 34, 34, 34, 34] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087872 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087872 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087872/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087872 Building REAL300004087873 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087873' /scratch/stefan/7774412/working/building/REAL300004087873 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087873 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087873/0 /scratch/stefan/7774412/working/building/REAL300004087873 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1110) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1110 `/scratch/stefan/7774412/working/3D/1110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC2=CC=CC=C2C=C1C=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087873 none COC1=NC2=CC=CC=C2C=C1C=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 2, 2, 2, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 7, 7, 2, 3, 3, 2, 2, 2] 40 rigid atoms, others: [16, 17, 18, 19, 20, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087873 none COC1=NC2=CC=CC=C2C=C1C=CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 40, 40, 40, 25, 25, 25, 4, 4, 4, 1, 1, 1, 1, 1, 10, 10, 25, 40, 40, 25, 25, 25] 40 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 34, 33, 30, 31] set([0, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 168 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087873 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087873 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087873/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087873 Building REAL300004087874 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087874' /scratch/stefan/7774412/working/building/REAL300004087874 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087874 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087874/0 /scratch/stefan/7774412/working/building/REAL300004087874 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1111) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1111 `/scratch/stefan/7774412/working/3D/1111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=NN2C)S1) `REAL300004087874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087874 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 25, 27, 27, 16, 16, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 16, 16, 16, 16, 25, 25, 16, 1, 1, 9, 9, 9, 9, 9] 43 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 112 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087874 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 16, 16, 16, 16, 16, 33, 33, 33, 33, 33, 1, 2, 2, 2, 2, 2, 2, 16, 16, 33, 33, 33, 33, 33] 43 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087874 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNN=C2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 43, 43, 43, 33, 33, 29, 9, 29, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 43, 43, 33, 9, 9, 1, 1, 2, 2, 2] 43 rigid atoms, others: [32, 33, 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, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087874 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087874 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087874/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087874 Building REAL300004087875 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087875' /scratch/stefan/7774412/working/building/REAL300004087875 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087875 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087875/0 /scratch/stefan/7774412/working/building/REAL300004087875 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1112) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1112 `/scratch/stefan/7774412/working/3D/1112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(=O)C2=CC=C(C)C=C2)S1) `REAL300004087875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087875 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 168, 201, 201, 201, 168, 75, 25, 6, 25, 1, 6, 1, 1, 1, 1, 1, 1, 1, 168, 168, 168, 168, 201, 201, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 33, 12, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087875 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 90, 90, 130, 130, 168, 168, 130, 132, 168, 168, 1, 2, 2, 2, 2, 2, 168, 168, 168, 168, 168, 168, 168] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087875 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087875/1 /scratch/stefan/7774412/working/building/REAL300004087875 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1113) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1113 `/scratch/stefan/7774412/working/3D/1113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(=O)C2=CC=C(C)C=C2)S1) `REAL300004087875.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087875/1/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: REAL300004087875 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 33, 33, 33, 25, 21, 19, 6, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 33, 33, 21, 1, 1, 2, 2, 2, 1, 1] 33 rigid atoms, others: [33, 34, 12, 14, 15, 16, 17, 18, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087875 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(=O)C2=CC=C(C)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 15, 15, 25, 25, 15, 23, 25, 25, 1, 2, 2, 2, 3, 3, 2, 25, 25, 25, 25, 25, 25, 25] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087875 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087875 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087875/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087875/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087875 Building REAL300004087876 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087876' /scratch/stefan/7774412/working/building/REAL300004087876 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087876 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087876/0 /scratch/stefan/7774412/working/building/REAL300004087876 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1114) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1114 `/scratch/stefan/7774412/working/3D/1114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(=O)C2=CC=C(Cl)C=C2)S1) `REAL300004087876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087876 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(=O)C2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 201, 201, 201, 163, 77, 27, 7, 27, 1, 7, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26]) total number of confs: 493 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087876 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(=O)C2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 81, 81, 117, 117, 163, 163, 133, 163, 163, 163, 1, 2, 2, 2, 2, 2, 163, 163, 163, 163] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 529 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087876 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087876/1 /scratch/stefan/7774412/working/building/REAL300004087876 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1115) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1115 `/scratch/stefan/7774412/working/3D/1115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(=O)C2=CC=C(Cl)C=C2)S1) `REAL300004087876.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087876/1/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: REAL300004087876 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(=O)C2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 10, 10, 10, 8, 8, 8, 5, 8, 1, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 10, 10, 8, 1, 1, 1, 1] 10 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087876 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(=O)C2=CC=C(Cl)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 11, 1, 1, 1, 1, 16, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 3, 3, 2, 8, 8, 8, 8] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087876 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087876 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087876/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087876/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087876 Building REAL300004087877 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087877' /scratch/stefan/7774412/working/building/REAL300004087877 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087877 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087877/0 /scratch/stefan/7774412/working/building/REAL300004087877 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1116) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1116 `/scratch/stefan/7774412/working/3D/1116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C2C(=N1)ON=C2C(C)C) `REAL300004087877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087877 none CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C2C(=N1)ON=C2C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 12, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5] 15 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087877 none CCC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C2C(=N1)ON=C2C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 12, 8, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 9, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 1, 5, 9, 9, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2] 15 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 22, 23, 24] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087877 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087877 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087877/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087877 Building REAL300004087878 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087878' /scratch/stefan/7774412/working/building/REAL300004087878 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087878 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087878/0 /scratch/stefan/7774412/working/building/REAL300004087878 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1117) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1117 `/scratch/stefan/7774412/working/3D/1117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=NC=N2)S1) `REAL300004087878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087878 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 31, 31, 31, 20, 20, 20, 8, 20, 8, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 31, 31, 20, 8, 8, 1, 1, 1] 31 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087878 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CC=NC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 8, 20, 20, 20, 20, 20, 1, 2, 2, 2, 2, 2, 2, 8, 8, 20, 20, 20] 31 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087878 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087878 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087878/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087878 Building REAL300004087879 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087879' /scratch/stefan/7774412/working/building/REAL300004087879 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087879 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087879/0 /scratch/stefan/7774412/working/building/REAL300004087879 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1118) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1118 `/scratch/stefan/7774412/working/3D/1118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC(C(C)C)=N2)S1) `REAL300004087879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087879 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC(C(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 26, 39, 39, 13, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 1, 13, 14, 14, 14, 26, 26, 10, 1, 13, 13, 13, 13, 13, 13, 13] 53 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 200 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087879 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC(C(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 34, 34, 13, 1, 2, 2, 2, 2, 2, 2, 13, 34, 34, 34, 34, 34, 34, 34] 53 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087879 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087879 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087879/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087879 Building REAL300004087880 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087880' /scratch/stefan/7774412/working/building/REAL300004087880 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087880 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087880/0 /scratch/stefan/7774412/working/building/REAL300004087880 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1119) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1119 `/scratch/stefan/7774412/working/3D/1119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCOCC1) `REAL300004087880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087880 none CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [9, 6, 1, 6, 18, 18, 19, 24, 24, 24, 45, 51, 51, 24, 24, 24, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 6, 19, 45, 45, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [2, 35, 36, 37, 38, 39, 40, 41, 42, 34, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 230 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087880 none CCC(C(=O)NC1=NC(CC(=O)[O-])=C(C)S1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 4, 2, 4, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 14, 24, 24, 24, 24, 24, 20, 20, 20, 20, 20, 14, 2, 3, 3, 2, 2, 2, 24, 24, 24, 24, 24, 24, 24, 24, 24] 51 rigid atoms, others: [5, 6, 7, 8, 9, 13, 14, 15] set([0, 1, 2, 3, 4, 10, 11, 12, 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: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087880 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087880 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087880/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087880 Building REAL300004087881 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087881' /scratch/stefan/7774412/working/building/REAL300004087881 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087881 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087881/0 /scratch/stefan/7774412/working/building/REAL300004087881 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1120) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1120 `/scratch/stefan/7774412/working/3D/1120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CC(OC(C)(C)C)C23CCC3)S1) `REAL300004087881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087881 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CC(OC(C)(C)C)C23CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [48, 34, 35, 36, 37, 12, 13, 14, 15, 16, 49, 50, 51, 52, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 34 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087881 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CC(OC(C)(C)C)C23CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 33 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087881 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087881 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087881/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087881 Building REAL300004087882 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087882' /scratch/stefan/7774412/working/building/REAL300004087882 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087882 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087882/0 /scratch/stefan/7774412/working/building/REAL300004087882 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1121) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1121 `/scratch/stefan/7774412/working/3D/1121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C(F)C=C(F)C=C23)S1) `REAL300004087882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087882 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C(F)C=C(F)C=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 15, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 34, 35, 35, 18, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 19, 19, 19, 34, 34, 13, 1, 1, 1] 35 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087882 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=COC3=C(F)C=C(F)C=C23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 1, 1, 15, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 2, 2, 2, 18, 18, 18] 35 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087882 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087882 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087882/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087882 Building REAL300004087883 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087883' /scratch/stefan/7774412/working/building/REAL300004087883 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087883 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087883/0 /scratch/stefan/7774412/working/building/REAL300004087883 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1122) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1122 `/scratch/stefan/7774412/working/3D/1122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(CC(F)(F)F)=N2)S1) `REAL300004087883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087883 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(CC(F)(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 5, 15, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 15, 15, 27, 51, 51, 15, 11, 9, 1, 9, 1, 1, 1, 1, 1, 8, 8, 8, 9, 1, 14, 15, 15, 15, 27, 27, 11, 1, 8, 8] 99 rigid atoms, others: [10, 12, 13, 14, 15, 16, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087883 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CSC(CC(F)(F)F)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 14, 1, 5, 5, 15, 15, 15, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 57, 57, 58, 57, 14, 1, 2, 2, 2, 2, 2, 2, 15, 57, 57] 99 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087883 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087883 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087883/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087883 Building REAL300004087884 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087884' /scratch/stefan/7774412/working/building/REAL300004087884 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087884 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087884/0 /scratch/stefan/7774412/working/building/REAL300004087884 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1123) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1123 `/scratch/stefan/7774412/working/3D/1123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=C21) `REAL300004087884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087884 none CCC1=CC=CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 14, 14, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 14, 27, 27, 27, 27, 27, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2] 43 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087884 none CCC1=CC=CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 14, 14, 14, 24, 27, 27, 14, 14, 14, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 24, 24, 15, 15, 15] 43 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 23, 24, 33, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 35, 36, 37, 38, 39, 40]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087884 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087884 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087884/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087884 Building REAL300004087885 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087885' /scratch/stefan/7774412/working/building/REAL300004087885 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087885 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087885/0 /scratch/stefan/7774412/working/building/REAL300004087885 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1124) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1124 `/scratch/stefan/7774412/working/3D/1124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C(F)(F)F)CC3)C=C2)S1) `REAL300004087885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087885 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C(F)(F)F)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 15, 15, 15, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 16, 16, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 7, 7, 7, 7, 1, 1] 36 rigid atoms, others: [32, 33, 38, 39, 10, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087885 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C(F)(F)F)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 15, 15, 15, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 7, 7, 4, 5, 21, 21, 21, 21, 21, 21, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 21, 21, 21, 21, 7, 7] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087885 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C3(C(F)(F)F)CC3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 15, 15, 15, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 36, 36, 36, 21, 17, 15, 4, 15, 1, 7, 7, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 21, 21, 21, 21, 36, 36, 17, 7, 7, 1, 1, 1, 1, 7, 7] 36 rigid atoms, others: [34, 35, 36, 37, 15, 16, 17, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 162 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087885 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087885 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087885/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087885 Building REAL300004087886 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087886' /scratch/stefan/7774412/working/building/REAL300004087886 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087886 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087886/0 /scratch/stefan/7774412/working/building/REAL300004087886 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1125) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1125 `/scratch/stefan/7774412/working/3D/1125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCS(=O)(=O)CC2)S1) `REAL300004087886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087886 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCS(=O)(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 105 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087886 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCS(=O)(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 53 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087886 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087886/1 /scratch/stefan/7774412/working/building/REAL300004087886 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1126) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1126 `/scratch/stefan/7774412/working/3D/1126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCS(=O)(=O)CC2)S1) `REAL300004087886.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087886/1/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: REAL300004087886 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCS(=O)(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 43, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 529 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087886 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCS(=O)(=O)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 14, 11, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 47, 47, 146, 146, 146, 146, 146, 146, 146, 146, 1, 2, 2, 2, 2, 2, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146, 146] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 400 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087886 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087886 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087886/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087886/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087886 Building REAL300004087887 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087887' /scratch/stefan/7774412/working/building/REAL300004087887 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087887 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087887/0 /scratch/stefan/7774412/working/building/REAL300004087887 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1127) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1127 `/scratch/stefan/7774412/working/3D/1127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C(C)(F)F)S1) `REAL300004087887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087887 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C(C)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 15, 15, 7, 7, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 11, 11, 7, 1, 1, 1, 1, 6, 6, 6] 19 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087887 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C(C)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 5, 7, 7, 7, 11, 11, 11, 1, 2, 2, 2, 2, 2, 2, 7, 7, 5, 7, 11, 11, 11] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087887 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087887 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087887/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087887 Building REAL300004087888 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087888' /scratch/stefan/7774412/working/building/REAL300004087888 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087888 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087888/0 /scratch/stefan/7774412/working/building/REAL300004087888 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1128) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1128 `/scratch/stefan/7774412/working/3D/1128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC=CC1) `REAL300004087888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087888 none C=CCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [35, 32, 10, 3, 3, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 10, 10, 10, 10, 35, 35, 35, 32, 32, 3, 2, 2, 1, 1, 1, 10, 10, 10, 10, 10, 10] 66 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087888 none C=CCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 7, 7, 7, 10, 10, 10, 19, 31, 31, 10, 10, 10, 1, 1, 1, 1, 11, 11, 11, 7, 7, 7, 19, 19, 10, 10, 10, 1, 1, 1, 1, 1, 1] 66 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 34, 17, 18, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 154 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087888 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087888/1 /scratch/stefan/7774412/working/building/REAL300004087888 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1129) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1129 `/scratch/stefan/7774412/working/3D/1129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CC=CC1) `REAL300004087888.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087888/1/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: REAL300004087888 none C=CCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [179, 165, 115, 41, 12, 41, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 115, 115, 115, 115, 179, 179, 179, 165, 165, 2, 2, 1, 1, 1, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087888 none C=CCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)CC=CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 1, 1, 1, 7, 7, 39, 115, 115, 115, 147, 174, 174, 115, 115, 115, 1, 1, 1, 1, 19, 19, 19, 8, 8, 147, 147, 115, 115, 115, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 17, 18, 19, 20, 36, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 510 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087888 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087888 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087888/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087888/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087888 Building REAL300004087889 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087889' /scratch/stefan/7774412/working/building/REAL300004087889 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087889 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087889/0 /scratch/stefan/7774412/working/building/REAL300004087889 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1130) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1130 `/scratch/stefan/7774412/working/3D/1130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCC2)S1) `REAL300004087889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087889 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 54, 84, 84, 29, 17, 13, 1, 13, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 29, 29, 29, 54, 54, 17, 1, 10, 10, 10, 10, 10, 10, 10] 111 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 355 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087889 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 29, 29, 29, 29, 29, 71, 71, 71, 1, 2, 2, 2, 2, 2, 2, 29, 71, 71, 71, 71, 71, 71, 71] 111 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087889 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 111, 111, 111, 71, 52, 47, 10, 47, 10, 10, 10, 10, 1, 1, 1, 1, 1, 71, 71, 71, 71, 111, 111, 52, 10, 1, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [32, 33, 34, 35, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 397 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087889 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087889 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087889/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087889 Building REAL300004087890 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087890' /scratch/stefan/7774412/working/building/REAL300004087890 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087890 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087890/0 /scratch/stefan/7774412/working/building/REAL300004087890 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1131) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1131 `/scratch/stefan/7774412/working/3D/1131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=NC(C4CC4)=NS3)C=N2)S1) `REAL300004087890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087890 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=NC(C4CC4)=NS3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 18, 31, 66, 66, 17, 14, 12, 1, 12, 1, 1, 1, 1, 7, 7, 7, 39, 39, 7, 7, 1, 1, 17, 18, 18, 18, 31, 31, 15, 1, 39, 39, 39, 39, 39, 1] 162 rigid atoms, others: [32, 38, 10, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 322 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087890 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=NC(C4CC4)=NS3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 17, 17, 17, 42, 42, 42, 119, 119, 42, 42, 17, 17, 1, 2, 2, 2, 2, 2, 2, 18, 119, 119, 119, 119, 119, 17] 162 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087890 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=NC(C4CC4)=NS3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 162, 162, 162, 119, 104, 100, 39, 100, 39, 39, 13, 13, 13, 1, 1, 1, 1, 13, 13, 39, 39, 119, 119, 119, 119, 162, 162, 104, 39, 1, 1, 1, 1, 1, 39] 162 rigid atoms, others: [33, 34, 35, 36, 37, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 528 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087890 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3=NC(C4CC4)=NS3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 5, 5, 8, 14, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [42, 42, 42, 42, 73, 125, 125, 42, 33, 31, 7, 31, 7, 7, 1, 1, 1, 1, 1, 13, 13, 1, 1, 7, 7, 42, 42, 42, 42, 73, 73, 33, 7, 13, 13, 13, 13, 13, 7] 162 rigid atoms, others: [14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 486 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087890 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087890 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087890/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087890 Building REAL300004087891 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087891' /scratch/stefan/7774412/working/building/REAL300004087891 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087891 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087891/0 /scratch/stefan/7774412/working/building/REAL300004087891 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1132) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1132 `/scratch/stefan/7774412/working/3D/1132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(F)CC2CCCC2)S1) `REAL300004087891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087891 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(F)CC2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 86, 86, 86, 57, 41, 38, 17, 38, 5, 17, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 86, 86, 41, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 346 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087891 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(F)CC2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 13, 13, 47, 57, 57, 57, 57, 1, 2, 2, 2, 2, 2, 3, 13, 49, 49, 57, 57, 57, 57, 57, 57, 57, 57, 57] 86 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087891 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087891/1 /scratch/stefan/7774412/working/building/REAL300004087891 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1133) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1133 `/scratch/stefan/7774412/working/3D/1133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(F)CC2CCCC2)S1) `REAL300004087891.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087891/1/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: REAL300004087891 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(F)CC2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 201, 201, 201, 171, 101, 52, 18, 52, 5, 18, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 201, 201, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087891 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(F)CC2CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 39, 39, 75, 75, 140, 171, 171, 171, 171, 1, 2, 2, 2, 2, 2, 75, 140, 140, 171, 171, 171, 171, 171, 171, 171, 171, 171] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087891 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087891 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087891/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087891/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087891 Building REAL300004087892 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087892' /scratch/stefan/7774412/working/building/REAL300004087892 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087892 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087892/0 /scratch/stefan/7774412/working/building/REAL300004087892 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1134) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1134 `/scratch/stefan/7774412/working/3D/1134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C)C2C(F)(F)F)S1) `REAL300004087892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087892 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C)C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 21, 21, 21, 12, 9, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 21, 21, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1] 21 rigid atoms, others: [38, 10, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087892 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC(C)(C)C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087892 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087892 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087892/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087892 Building REAL300004087893 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087893' /scratch/stefan/7774412/working/building/REAL300004087893 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087893 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087893/0 /scratch/stefan/7774412/working/building/REAL300004087893 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1135) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1135 `/scratch/stefan/7774412/working/3D/1135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1) `REAL300004087893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087893 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 14, 14, 6, 5, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 6, 11, 11, 5, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [45, 38, 39, 40, 41, 10, 43, 12, 13, 44, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 74 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: REAL300004087893 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 3, 3, 6, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 3, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087893 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 16, 16, 16, 10, 9, 9, 7, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 10, 10, 16, 16, 9, 2, 2, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 16 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087893 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087893/1 /scratch/stefan/7774412/working/building/REAL300004087893 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1136) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1136 `/scratch/stefan/7774412/working/3D/1136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1) `REAL300004087893.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087893 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 188, 197, 197, 139, 38, 7, 1, 7, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 139, 139, 139, 139, 188, 188, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 12, 13, 44, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 529 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087893 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 61, 61, 139, 153, 153, 153, 153, 153, 153, 153, 139, 139, 139, 139, 1, 2, 2, 2, 2, 2, 153, 153, 153, 153, 153, 153, 139, 139, 139, 139, 139, 139, 139, 139] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087893 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 201, 201, 201, 153, 50, 15, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 153, 153, 153, 153, 201, 201, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 506 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087893 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087893 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087893/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087893/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087893 Building REAL300004087894 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087894' /scratch/stefan/7774412/working/building/REAL300004087894 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087894 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087894/0 /scratch/stefan/7774412/working/building/REAL300004087894 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1137) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1137 `/scratch/stefan/7774412/working/3D/1137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCCC2CC(=O)CC3)S1) `REAL300004087894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087894 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCCC2CC(=O)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 51 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087894 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCCC2CC(=O)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087894 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087894/1 /scratch/stefan/7774412/working/building/REAL300004087894 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1138) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1138 `/scratch/stefan/7774412/working/3D/1138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCCC2CC(=O)CC3)S1) `REAL300004087894.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087894/1/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: REAL300004087894 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCCC2CC(=O)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 147, 147, 147, 107, 23, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 147, 147, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 147 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087894 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCCC2CC(=O)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 61, 61, 107, 107, 107, 107, 107, 107, 107, 107, 107, 1, 2, 2, 2, 2, 2, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107] 147 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087894 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087894 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087894/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087894/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087894 Building REAL300004087895 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087895' /scratch/stefan/7774412/working/building/REAL300004087895 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087895 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087895/0 /scratch/stefan/7774412/working/building/REAL300004087895 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1139) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1139 `/scratch/stefan/7774412/working/3D/1139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CC2)S1) `REAL300004087895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087895 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 27, 32, 32, 14, 8, 7, 1, 7, 1, 1, 8, 8, 8, 8, 1, 1, 14, 14, 14, 14, 27, 27, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 52 rigid atoms, others: [34, 35, 36, 37, 10, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 145 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087895 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 14, 28, 28, 28, 28, 14, 14, 1, 2, 2, 2, 2, 2, 3, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14] 52 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087895 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 52, 52, 52, 28, 20, 19, 8, 19, 1, 1, 1, 1, 1, 1, 8, 8, 28, 28, 28, 28, 52, 52, 20, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 52 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37]) total number of confs: 215 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087895 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087895/1 /scratch/stefan/7774412/working/building/REAL300004087895 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1140) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1140 `/scratch/stefan/7774412/working/3D/1140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CC2)S1) `REAL300004087895.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087895 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 14, 14, 14, 12, 6, 3, 1, 3, 1, 1, 4, 4, 4, 4, 1, 1, 12, 12, 12, 12, 14, 14, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1] 14 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087895 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 7, 12, 12, 12, 14, 14, 14, 14, 12, 12, 1, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 12] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087895 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 8, 5, 4, 5, 1, 1, 1, 1, 1, 1, 4, 4, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 14 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36]) total number of confs: 28 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087895 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087895 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087895/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087895/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087895 Building REAL300004087896 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087896' /scratch/stefan/7774412/working/building/REAL300004087896 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087896 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087896/0 /scratch/stefan/7774412/working/building/REAL300004087896 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1141) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1141 `/scratch/stefan/7774412/working/3D/1141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1) `REAL300004087896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087896 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 21, 21, 7, 5, 5, 1, 5, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 5, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 46, 44, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087896 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 7, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7] 36 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087896 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 36, 36, 36, 20, 15, 15, 8, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 20, 20, 20, 20, 36, 36, 15, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 36 rigid atoms, others: [33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 145 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087896 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087896/1 /scratch/stefan/7774412/working/building/REAL300004087896 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1142) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1142 `/scratch/stefan/7774412/working/3D/1142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1) `REAL300004087896.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087896 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 143, 157, 157, 99, 27, 7, 1, 7, 1, 1, 5, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 99, 99, 99, 99, 143, 143, 5, 5, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [45, 38, 39, 40, 41, 10, 43, 12, 13, 44, 21, 22, 23, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087896 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 58, 58, 99, 160, 160, 160, 160, 160, 160, 160, 99, 99, 99, 99, 99, 1, 2, 2, 2, 2, 2, 160, 160, 160, 160, 160, 160, 99, 99, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087896 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 160, 160, 201, 201, 201, 160, 63, 18, 5, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 160, 160, 160, 160, 201, 201, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 6, 5, 6, 5] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 500 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087896 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087896 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087896/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087896/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087896 Building REAL300004087897 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087897' /scratch/stefan/7774412/working/building/REAL300004087897 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087897 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087897/0 /scratch/stefan/7774412/working/building/REAL300004087897 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1143) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1143 `/scratch/stefan/7774412/working/3D/1143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CCCO3)S1) `REAL300004087897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087897 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CCCO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087897 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3(C2)CCCO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087897 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087897 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087897/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087897 Building REAL300004087898 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087898' /scratch/stefan/7774412/working/building/REAL300004087898 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087898 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087898/0 /scratch/stefan/7774412/working/building/REAL300004087898 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1144) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1144 `/scratch/stefan/7774412/working/3D/1144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H](C)C2=CC=C(C(F)(F)F)C=C2)S1) `REAL300004087898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087898 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H](C)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 12, 12, 12, 9, 9, 9, 8, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9, 9, 9, 9, 12, 12, 9, 8, 8, 5, 5, 5, 1, 1, 1, 1] 12 rigid atoms, others: [38, 39, 40, 41, 13, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087898 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H](C)C2=CC=C(C(F)(F)F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 2, 2, 3, 6, 6, 6, 9, 9, 6, 6, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 3, 3, 6, 6, 6, 9, 9, 9, 9] 12 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087898 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087898 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087898/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087898 Building REAL300004087899 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087899' /scratch/stefan/7774412/working/building/REAL300004087899 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087899 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087899/0 /scratch/stefan/7774412/working/building/REAL300004087899 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1145) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1145 `/scratch/stefan/7774412/working/3D/1145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H](C)C2=CC=C3OCOC3=C2)S1) `REAL300004087899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087899 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H](C)C2=CC=C3OCOC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 16, 16, 16, 9, 9, 9, 8, 9, 4, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 9, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1] 16 rigid atoms, others: [37, 38, 39, 40, 41, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087899 none CC1=C(CC(=O)[O-])N=C(NC(=O)C[C@H](C)C2=CC=C3OCOC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 7, 5, 1, 1, 1, 1, 12, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 3, 3, 5, 5, 5, 9, 9, 9, 9, 9] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087899 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087899 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087899/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087899 Building REAL300004087900 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087900' /scratch/stefan/7774412/working/building/REAL300004087900 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087900 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087900/0 /scratch/stefan/7774412/working/building/REAL300004087900 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1146) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1146 `/scratch/stefan/7774412/working/3D/1146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=CCC1) `REAL300004087900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087900 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 12, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 12, 12, 12, 12, 30, 30, 30, 30, 30, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12] 55 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087900 none COCC1(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 1, 1, 1, 7, 7, 7, 12, 12, 12, 23, 23, 23, 12, 12, 12, 1, 1, 1, 1, 9, 9, 9, 7, 7, 7, 23, 23, 12, 12, 12, 1, 1, 1, 1, 1, 1] 55 rigid atoms, others: [32, 33, 2, 3, 4, 37, 35, 34, 17, 18, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 116 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087900 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087900/1 /scratch/stefan/7774412/working/building/REAL300004087900 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1147) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1147 `/scratch/stefan/7774412/working/3D/1147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=CCC1) `REAL300004087900.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087900/1/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: REAL300004087900 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [168, 148, 134, 50, 13, 50, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 134, 134, 134, 134, 168, 168, 168, 148, 148, 2, 2, 2, 2, 2, 134, 134, 134, 134, 134, 134] 201 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 500 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087900 none COCC1(C(=O)[N-]C2=NC(CC(=O)[O-])=C(C)S2)C=CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 7, 7, 37, 134, 134, 134, 194, 197, 197, 134, 134, 134, 1, 1, 1, 1, 10, 10, 10, 6, 6, 194, 194, 134, 134, 134, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 17, 18, 19, 20, 36, 31] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 566 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087900 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087900 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087900/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087900/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087900 Building REAL300004087901 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087901' /scratch/stefan/7774412/working/building/REAL300004087901 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087901 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087901/0 /scratch/stefan/7774412/working/building/REAL300004087901 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1148) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1148 `/scratch/stefan/7774412/working/3D/1148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(F)(F)F)CCCCO2)S1) `REAL300004087901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087901 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(F)(F)F)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 10, 10, 10, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087901 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C(F)(F)F)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6] 10 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087901 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087901/1 /scratch/stefan/7774412/working/building/REAL300004087901 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1149) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1149 `/scratch/stefan/7774412/working/3D/1149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(F)(F)F)CCCCO2)S1) `REAL300004087901.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087901/1/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: REAL300004087901 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(F)(F)F)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 193, 193, 193, 139, 34, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 193, 193, 1, 1, 1, 1, 1, 1, 1, 1] 193 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087901 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C(F)(F)F)CCCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 15, 15, 15, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 70, 70, 139, 139, 139, 139, 139, 139, 139, 139, 139, 1, 2, 2, 2, 2, 2, 139, 139, 139, 139, 139, 139, 139, 139] 193 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087901 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087901 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087901/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087901/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087901 Building REAL300004087902 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087902' /scratch/stefan/7774412/working/building/REAL300004087902 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087902 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087902/0 /scratch/stefan/7774412/working/building/REAL300004087902 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1150) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1150 `/scratch/stefan/7774412/working/3D/1150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1) `REAL300004087902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087902 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 36, 38, 38, 19, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 3, 3, 19, 19, 19, 19, 36, 36, 13, 1, 1, 1, 1, 3, 3, 3, 3] 38 rigid atoms, others: [33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 159 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087902 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 21, 21, 21, 1, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 21, 21, 21, 21] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087902 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 38, 38, 38, 21, 16, 14, 3, 14, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 38, 38, 16, 3, 3, 3, 3, 1, 1, 1, 1] 38 rigid atoms, others: [37, 38, 39, 40, 17, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 153 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087902 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087902/1 /scratch/stefan/7774412/working/building/REAL300004087902 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1151) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1151 `/scratch/stefan/7774412/working/3D/1151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1) `REAL300004087902.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087902 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 201, 201, 201, 150, 47, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 150, 150, 150, 150, 201, 201, 1, 1, 1, 1, 3, 3, 3, 3] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 518 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087902 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 70, 70, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 150, 1, 2, 2, 2, 2, 2, 150, 150, 150, 150, 150, 150, 150, 150] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 422 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087902 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCO[C@H]2C2=CC=C(F)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 201, 201, 201, 150, 50, 15, 3, 15, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 150, 150, 150, 150, 201, 201, 3, 3, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 17, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 522 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087902 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087902 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087902/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087902/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087902 Building REAL300004087903 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087903' /scratch/stefan/7774412/working/building/REAL300004087903 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087903 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087903/0 /scratch/stefan/7774412/working/building/REAL300004087903 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1152) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1152 `/scratch/stefan/7774412/working/3D/1152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C(C)C)C(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087903 none CC1=NN(C(C)C)C(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 21, 21, 20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 20, 20, 20, 2, 2, 2, 2, 2, 2] 35 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 61 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087903 none CC1=NN(C(C)C)C(C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 5, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 11, 11, 13, 20, 20, 20, 35, 35, 35, 20, 20, 20, 2, 2, 2, 3, 4, 4, 4, 4, 4, 4, 2, 2, 2, 13, 35, 35, 20, 20, 20] 35 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087903 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087903 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087903/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087903 Building REAL300004087904 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087904' /scratch/stefan/7774412/working/building/REAL300004087904 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087904 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087904/0 /scratch/stefan/7774412/working/building/REAL300004087904 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1153) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1153 `/scratch/stefan/7774412/working/3D/1153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCCO2)S1) `REAL300004087904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087904 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 47, 71, 71, 24, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 25, 25, 25, 47, 47, 14, 1, 10, 10, 10, 10, 10, 10, 10] 103 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 305 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087904 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 24, 24, 24, 69, 69, 69, 69, 1, 2, 2, 2, 2, 2, 2, 24, 69, 69, 69, 69, 69, 69, 69] 103 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087904 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CON=C2C2CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 12, 8, 1, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 103, 103, 103, 69, 58, 56, 10, 56, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 103, 103, 58, 10, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [32, 33, 34, 35, 36, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 355 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087904 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087904 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087904/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087904 Building REAL300004087905 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087905' /scratch/stefan/7774412/working/building/REAL300004087905 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087905 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087905/0 /scratch/stefan/7774412/working/building/REAL300004087905 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1154) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1154 `/scratch/stefan/7774412/working/3D/1154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCCC3(CCC3)O2)S1) `REAL300004087905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087905 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCCC3(CCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 39, 39, 39, 23, 22, 20, 7, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 39, 39, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 162 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087905 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2CCCC3(CCC3)O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 15, 22, 23, 23, 23, 23, 23, 23, 23, 1, 2, 2, 2, 2, 2, 2, 15, 15, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 39 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087905 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087905 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087905/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087905 Building REAL300004087906 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087906' /scratch/stefan/7774412/working/building/REAL300004087906 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087906 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087906/0 /scratch/stefan/7774412/working/building/REAL300004087906 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1155) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1155 `/scratch/stefan/7774412/working/3D/1155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1C[C@@H]2CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C[C@H]12) `REAL300004087906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087906 none COC1C[C@@H]2CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 20, 20, 20, 20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 31, 31, 31, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 20, 20] 44 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 93 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087906 none COC1C[C@@H]2CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 7, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 20, 20, 20, 37, 44, 44, 20, 20, 20, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 14, 37, 37, 20, 20, 20, 1, 1] 44 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 40, 21, 22, 23, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087906 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087906 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087906/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087906 Building REAL300004087907 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087907' /scratch/stefan/7774412/working/building/REAL300004087907 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087907 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087907/0 /scratch/stefan/7774412/working/building/REAL300004087907 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1156) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1156 `/scratch/stefan/7774412/working/3D/1156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCCN2CC(F)(F)F)S1) `REAL300004087907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087907 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCCN2CC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 10, 5, 5, 15, 15, 15, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 15, 15, 15, 9, 7, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 9, 9, 15, 15, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4] 15 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41]) total number of confs: 75 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087907 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCCN2CC(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 10, 5, 5, 15, 15, 15, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 8, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 8, 8, 9, 9, 9, 9, 9, 9, 9, 10, 10] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087907 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087907 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087907/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087907 Building REAL300004087908 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087908' /scratch/stefan/7774412/working/building/REAL300004087908 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087908 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087908/0 /scratch/stefan/7774412/working/building/REAL300004087908 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1157) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1157 `/scratch/stefan/7774412/working/3D/1157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2CCC3=CC=CC=C32)S1) `REAL300004087908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087908 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 38, 38, 38, 24, 15, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 38, 38, 15, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 139 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: REAL300004087908 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 2, 2, 3, 24, 24, 24, 24, 24, 24, 24, 24] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087908 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087908/1 /scratch/stefan/7774412/working/building/REAL300004087908 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1158) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1158 `/scratch/stefan/7774412/working/3D/1158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H]2CCC3=CC=CC=C32)S1) `REAL300004087908.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087908/1/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: REAL300004087908 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 149, 149, 201, 201, 201, 149, 48, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 149, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087908 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 66, 66, 149, 149, 149, 149, 149, 149, 149, 149, 149, 1, 2, 2, 2, 2, 2, 149, 149, 149, 149, 149, 149, 149, 149] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 427 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087908 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087908 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087908/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087908/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087908 Building REAL300004087909 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087909' /scratch/stefan/7774412/working/building/REAL300004087909 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087909 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087909/0 /scratch/stefan/7774412/working/building/REAL300004087909 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1159) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1159 `/scratch/stefan/7774412/working/3D/1159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC23CCC(CC2)C3(C)C)S1) `REAL300004087909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087909 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 19, 19, 19, 10, 10, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087909 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC23CCC(CC2)C3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087909 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087909 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087909/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087909 Building REAL300004087910 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087910' /scratch/stefan/7774412/working/building/REAL300004087910 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087910 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087910/0 /scratch/stefan/7774412/working/building/REAL300004087910 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1160) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1160 `/scratch/stefan/7774412/working/3D/1160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C3CCOC3)C=N2)S1) `REAL300004087910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087910 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C3CCOC3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 12, 5, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 11, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 9, 9, 5, 5, 5, 1, 5, 5, 5, 5, 5, 5, 5, 1] 33 rigid atoms, others: [32, 40, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087910 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C3CCOC3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 12, 5, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 17, 17, 17, 17, 5, 5, 1, 2, 2, 2, 2, 2, 2, 2, 2, 5, 17, 17, 17, 17, 17, 17, 17, 5] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087910 none CC1=C(CC(=O)[O-])N=C(NC(=O)CN2C=C(C3CCOC3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 12, 5, 1, 8, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 33, 33, 33, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 17, 17, 17, 17, 33, 33, 17, 17, 17, 5, 1, 1, 1, 1, 1, 1, 1, 5] 33 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40]) total number of confs: 150 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087910 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087910/1 /scratch/stefan/7774412/working/building/REAL300004087910 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1161) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1161 `/scratch/stefan/7774412/working/3D/1161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C3CCOC3)C=N2)S1) `REAL300004087910.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087910 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C3CCOC3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 12, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 88, 96, 96, 72, 44, 23, 7, 23, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 72, 72, 72, 72, 88, 88, 7, 7, 1, 8, 8, 8, 8, 8, 8, 8, 1] 201 rigid atoms, others: [39, 12, 13, 14, 15, 16, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087910 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C3CCOC3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 12, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 10, 24, 24, 50, 72, 72, 72, 175, 175, 175, 175, 72, 72, 1, 2, 2, 2, 2, 2, 50, 50, 72, 175, 175, 175, 175, 175, 175, 175, 72] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087910 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CN2C=C(C3CCOC3)C=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 12, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 201, 201, 201, 175, 128, 72, 24, 72, 8, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 175, 175, 175, 175, 201, 201, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 8] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39]) total number of confs: 543 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087910 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087910 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087910/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087910/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087910 Building REAL300004087911 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087911' /scratch/stefan/7774412/working/building/REAL300004087911 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087911 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087911/0 /scratch/stefan/7774412/working/building/REAL300004087911 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1162) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1162 `/scratch/stefan/7774412/working/3D/1162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CNC3=NC=C2)S1) `REAL300004087911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087911 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CNC3=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 27, 27, 27, 16, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 27, 27, 12, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087911 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CNC3=NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087911 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087911/1 /scratch/stefan/7774412/working/building/REAL300004087911 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1163) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1163 `/scratch/stefan/7774412/working/3D/1163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CN=C3NC=C2)S1) `REAL300004087911.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087911/1/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: REAL300004087911 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CN=C3NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 13, 13, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 7, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087911 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CN=C3NC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 7, 7] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 34 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087911 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087911 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087911/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087911/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087911 Building REAL300004087912 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087912' /scratch/stefan/7774412/working/building/REAL300004087912 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087912 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087912/0 /scratch/stefan/7774412/working/building/REAL300004087912 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1164) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1164 `/scratch/stefan/7774412/working/3D/1164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=CC=C2O1) `REAL300004087912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087912 none CC1=CC2=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13] 23 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087912 none CC1=CC2=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=CC=C2O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 23, 23, 23, 13, 13, 13, 1, 1, 1, 1, 1, 2, 2, 2, 1, 9, 23, 23, 13, 13, 13, 1, 1, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 33, 34, 18, 19, 20, 21, 22, 26] set([32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 27, 28, 29, 30, 31]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087912 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087912 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087912/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087912 Building REAL300004087913 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087913' /scratch/stefan/7774412/working/building/REAL300004087913 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087913 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087913/0 /scratch/stefan/7774412/working/building/REAL300004087913 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1165) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1165 `/scratch/stefan/7774412/working/3D/1165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3(CCC3)CC2)S1) `REAL300004087913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087913 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3(CCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 15, 15, 29, 29, 29, 15, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 15, 15, 15, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 29 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 122 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087913 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3(CCC3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2, 3, 3, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087913 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087913 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087913/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087913 Building REAL300004087914 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087914' /scratch/stefan/7774412/working/building/REAL300004087914 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087914 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087914/0 /scratch/stefan/7774412/working/building/REAL300004087914 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1166) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1166 `/scratch/stefan/7774412/working/3D/1166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC2=C(OCC2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1) `REAL300004087914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087914 none CCC1=CC2=C(OCC2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [22, 14, 14, 14, 14, 14, 14, 14, 14, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 14, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 14] 36 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 96 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087914 none CCC1=CC2=C(OCC2)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 12, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 14, 14, 14, 22, 22, 22, 14, 14, 14, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 13, 22, 22, 14, 14, 14, 1] 36 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 40, 23, 33, 29, 30, 31] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087914 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087914 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087914/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087914 Building REAL300004087915 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087915' /scratch/stefan/7774412/working/building/REAL300004087915 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087915 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087915/0 /scratch/stefan/7774412/working/building/REAL300004087915 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1167) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1167 `/scratch/stefan/7774412/working/3D/1167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CSC3=CC=C2)S1) `REAL300004087915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087915 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CSC3=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 14, 14, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 8, 1, 1, 1, 1, 1] 14 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087915 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C3C=CSC3=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087915 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087915 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087915/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087915 Building REAL300004087916 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087916' /scratch/stefan/7774412/working/building/REAL300004087916 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087916 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087916/0 /scratch/stefan/7774412/working/building/REAL300004087916 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1168) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1168 `/scratch/stefan/7774412/working/3D/1168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3C=C(Cl)C=N3)C=C2)S1) `REAL300004087916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087916 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3C=C(Cl)C=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 16, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 11, 15, 15, 6, 4, 4, 1, 4, 1, 1, 1, 1, 1, 8, 29, 29, 29, 29, 29, 1, 1, 6, 6, 6, 6, 11, 11, 4, 1, 1, 8, 8, 29, 29, 1, 1] 101 rigid atoms, others: [32, 33, 38, 39, 10, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37]) total number of confs: 108 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087916 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3C=C(Cl)C=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 16, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 6, 6, 4, 3, 25, 57, 57, 57, 57, 57, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 25, 25, 57, 57, 6, 6] 101 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087916 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(CN3C=C(Cl)C=N3)C=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 1, 16, 1, 8, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 101, 101, 101, 57, 51, 51, 29, 51, 29, 29, 29, 9, 1, 1, 1, 1, 1, 1, 1, 29, 29, 57, 57, 57, 57, 101, 101, 51, 29, 29, 9, 9, 1, 1, 29, 29] 101 rigid atoms, others: [36, 37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 408 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087916 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087916 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087916/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087916 Building REAL300004087917 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087917' /scratch/stefan/7774412/working/building/REAL300004087917 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087917 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087917/0 /scratch/stefan/7774412/working/building/REAL300004087917 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1169) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1169 `/scratch/stefan/7774412/working/3D/1169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(F)(F)F)=CS2)S1) `REAL300004087917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087917 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(F)(F)F)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 13, 13, 25, 25, 25, 13, 8, 8, 1, 8, 1, 1, 1, 1, 2, 2, 2, 1, 1, 12, 13, 13, 13, 25, 25, 8, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087917 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C(F)(F)F)=CS2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 15, 15, 15, 1, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 13, 13, 13, 13, 12, 12, 1, 2, 2, 2, 2, 2, 2, 13, 12] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087917 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087917 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087917/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087917 Building REAL300004087918 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087918' /scratch/stefan/7774412/working/building/REAL300004087918 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087918 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087918/0 /scratch/stefan/7774412/working/building/REAL300004087918 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1170) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1170 `/scratch/stefan/7774412/working/3D/1170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC3CC3)=C2)S1) `REAL300004087918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087918 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 17, 36, 36, 9, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 5, 13, 34, 34, 1, 9, 9, 9, 9, 17, 17, 7, 1, 1, 1, 13, 13, 34, 34, 34, 34, 34, 1] 201 rigid atoms, others: [32, 40, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 234 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087918 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 31, 60, 127, 127, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 60, 60, 127, 127, 127, 127, 127, 9] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 421 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087918 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(OCC3CC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 201, 201, 201, 127, 123, 123, 34, 123, 34, 34, 34, 34, 21, 10, 1, 1, 1, 1, 34, 127, 127, 127, 127, 201, 201, 123, 34, 34, 34, 10, 10, 1, 1, 1, 1, 1, 34] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40]) total number of confs: 754 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087918 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087918 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087918/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087918 Building REAL300004087919 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087919' /scratch/stefan/7774412/working/building/REAL300004087919 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087919 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087919/0 /scratch/stefan/7774412/working/building/REAL300004087919 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1171) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1171 `/scratch/stefan/7774412/working/3D/1171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(Cl)=C1) `REAL300004087919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087919 none CSC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 13, 13, 13, 3, 3, 2, 2, 2, 2, 2, 2, 3] 13 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087919 none CSC1=CC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 9, 9, 3, 3, 3, 1, 1, 1, 9, 9, 9, 1, 1, 3, 5, 5, 3, 3, 3, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 19, 20, 21, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087919 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087919 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087919/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087919 Building REAL300004087920 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087920' /scratch/stefan/7774412/working/building/REAL300004087920 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087920 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087920/0 /scratch/stefan/7774412/working/building/REAL300004087920 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1172) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1172 `/scratch/stefan/7774412/working/3D/1172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C(C)(F)F)=C2)S1) `REAL300004087920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087920 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C(C)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 47, 47, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 7, 7, 7, 1] 89 rigid atoms, others: [35, 10, 12, 13, 14, 15, 16, 17, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34]) total number of confs: 195 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087920 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C(C)(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 3, 13, 13, 47, 47, 47, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 3, 47, 47, 47, 13] 89 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087920 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087920 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087920/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087920 Building REAL300004087921 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087921' /scratch/stefan/7774412/working/building/REAL300004087921 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087921 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087921/0 /scratch/stefan/7774412/working/building/REAL300004087921 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1173) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1173 `/scratch/stefan/7774412/working/3D/1173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=CSC3=C2)S1) `REAL300004087921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087921 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=CSC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087921 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3C=CSC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087921 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087921 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087921/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087921 Building REAL300004087922 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087922' /scratch/stefan/7774412/working/building/REAL300004087922 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087922 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087922/0 /scratch/stefan/7774412/working/building/REAL300004087922 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1174) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1174 `/scratch/stefan/7774412/working/3D/1174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NN2C)S1) `REAL300004087922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087922 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 23, 25, 25, 14, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 14, 14, 23, 23, 14, 1, 2, 2, 2, 9, 9, 9, 9, 9] 45 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087922 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 14, 14, 31, 31, 31, 31, 31, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 31, 31, 31, 31, 31] 45 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087922 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C)N=C2C2=CC=NN2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 8, 1, 1, 1, 1, 8, 8, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 45, 45, 45, 31, 31, 29, 9, 29, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 45, 45, 31, 9, 9, 9, 9, 1, 1, 2, 2, 2] 45 rigid atoms, others: [35, 36, 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, 37, 38, 39]) total number of confs: 160 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087922 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087922 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087922/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087922 Building REAL300004087923 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087923' /scratch/stefan/7774412/working/building/REAL300004087923 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087923 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087923/0 /scratch/stefan/7774412/working/building/REAL300004087923 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1175) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1175 `/scratch/stefan/7774412/working/3D/1175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=CO1) `REAL300004087923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087923 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [51, 25, 25, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 25, 25, 25, 25, 52, 52, 52, 51, 51, 2, 2, 2, 2, 2, 2, 26, 26, 26, 25] 77 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 216 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087923 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 12, 12, 14, 25, 25, 25, 50, 53, 53, 25, 25, 25, 1, 1, 1, 1, 8, 8, 8, 7, 7, 14, 50, 50, 26, 26, 26, 2, 2, 2, 1] 77 rigid atoms, others: [1, 2, 3, 4, 35, 17, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 256 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087923 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087923 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087923/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087923 Building REAL300004087924 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087924' /scratch/stefan/7774412/working/building/REAL300004087924 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087924 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087924/0 /scratch/stefan/7774412/working/building/REAL300004087924 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1176) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1176 `/scratch/stefan/7774412/working/3D/1176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NC(C)=NC=C3C2)S1) `REAL300004087924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087924 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NC(C)=NC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 5, 8, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 8, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 37, 35, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087924 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3=NC(C)=NC=C3C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 1, 8, 1, 5, 8, 1, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087924 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087924 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087924/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087924 Building REAL300004087925 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087925' /scratch/stefan/7774412/working/building/REAL300004087925 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087925 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087925/0 /scratch/stefan/7774412/working/building/REAL300004087925 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1177) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1177 `/scratch/stefan/7774412/working/3D/1177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C(F)(F)F)=CO1) `REAL300004087925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087925 none CC1=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C(F)(F)F)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 2, 3, 3, 2, 2, 2, 7] 11 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087925 none CC1=C(CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C(F)(F)F)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 6, 7, 7, 7, 7, 11, 11, 11, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 7, 11, 11, 7, 7, 7, 1] 11 rigid atoms, others: [0, 1, 2, 3, 17, 18, 35, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087925 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087925 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087925/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087925 Building REAL300004087926 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087926' /scratch/stefan/7774412/working/building/REAL300004087926 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087926 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087926/0 /scratch/stefan/7774412/working/building/REAL300004087926 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1178) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1178 `/scratch/stefan/7774412/working/3D/1178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(C)=N1) `REAL300004087926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087926 none COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'N.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, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 13, 13, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 13, 13, 13, 17, 17, 17, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 33 rigid atoms, others: [7, 8, 9, 10, 11, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087926 none COC1=CC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CC(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.3', 'N.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, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 7, 7, 9, 13, 13, 13, 25, 25, 25, 13, 13, 13, 1, 1, 1, 1, 3, 3, 3, 1, 9, 25, 25, 13, 13, 13, 1, 2, 2, 2] 33 rigid atoms, others: [32, 1, 2, 3, 4, 5, 18, 19, 20, 21, 25] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087926 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087926 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087926/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087926 Building REAL300004087927 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087927' /scratch/stefan/7774412/working/building/REAL300004087927 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087927 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087927/0 /scratch/stefan/7774412/working/building/REAL300004087927 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1179) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1179 `/scratch/stefan/7774412/working/3D/1179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)N=C1) `REAL300004087927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087927 none CC1=CN(CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 25, 25, 11, 11, 11, 1, 1, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 7, 21, 21, 11, 11, 11, 1, 1, 15] 115 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 40, 41, 22, 23] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 124 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087927 none CC1=CN(CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 15, 15, 15, 15, 51, 51, 51, 63, 63, 63, 115, 115, 115, 63, 63, 63, 15, 15, 1, 1, 2, 2, 2, 1, 9, 9, 15, 15, 51, 115, 115, 63, 63, 63, 15, 15, 1] 115 rigid atoms, others: [0, 1, 2, 3, 4, 42, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087927 none CC1=CN(CC2=CC=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 29, 3, 4, 11, 11, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 11, 11, 63, 63, 63, 63, 63, 63, 29, 29, 11, 11, 2, 2, 2, 2, 2, 2, 11, 11, 63] 115 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 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: 201 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087927 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087927 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087927/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087927 Building REAL300004087928 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087928' /scratch/stefan/7774412/working/building/REAL300004087928 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087928 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087928/0 /scratch/stefan/7774412/working/building/REAL300004087928 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1180) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1180 `/scratch/stefan/7774412/working/3D/1180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCCC2CCC3)S1) `REAL300004087928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087928 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCCC2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 19, 19, 19, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 75 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087928 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CCCC2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 19 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 37 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087928 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087928/1 /scratch/stefan/7774412/working/building/REAL300004087928 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1181) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1181 `/scratch/stefan/7774412/working/3D/1181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCCC2CCC3)S1) `REAL300004087928.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087928/1/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: REAL300004087928 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCCC2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 153, 153, 201, 201, 201, 153, 42, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25]) total number of confs: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087928 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CCCC2CCC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 47, 47, 153, 153, 153, 153, 153, 153, 153, 1, 2, 2, 2, 2, 2, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153, 153] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087928 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087928 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087928/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087928/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087928 Building REAL300004087929 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087929' /scratch/stefan/7774412/working/building/REAL300004087929 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087929 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087929/0 /scratch/stefan/7774412/working/building/REAL300004087929 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1182) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1182 `/scratch/stefan/7774412/working/3D/1182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1) `REAL300004087929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087929 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 23, 26, 26, 12, 8, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 12, 12, 12, 12, 23, 23, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 114 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087929 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 14, 14, 12, 14, 14, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 14, 14, 12, 14, 14] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087929 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 26, 26, 14, 10, 8, 3, 8, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 10, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 26 rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087929 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087929/1 /scratch/stefan/7774412/working/building/REAL300004087929 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1183) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1183 `/scratch/stefan/7774412/working/3D/1183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1) `REAL300004087929.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087929 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 192, 201, 201, 131, 31, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 131, 131, 131, 131, 192, 192, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42]) total number of confs: 575 number of broken/clashed sets: 121 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087929 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 89, 89, 131, 131, 131, 131, 131, 131, 131, 131, 142, 142, 131, 142, 142, 1, 2, 2, 2, 3, 3, 131, 131, 131, 131, 131, 131, 142, 142, 131, 142, 142] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 427 number of broken/clashed sets: 121 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087929 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 201, 201, 201, 142, 41, 8, 3, 8, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 201, 201, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 543 number of broken/clashed sets: 121 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087929 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087929 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087929/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087929/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087929 Building REAL300004087930 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087930' /scratch/stefan/7774412/working/building/REAL300004087930 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087930 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087930/0 /scratch/stefan/7774412/working/building/REAL300004087930 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1184) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1184 `/scratch/stefan/7774412/working/3D/1184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1) `REAL300004087930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087930 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 29, 38, 38, 16, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 16, 16, 16, 16, 29, 29, 12, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3] 38 rigid atoms, others: [33, 34, 35, 36, 37, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087930 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 22, 22, 22, 22, 22, 1, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 22, 22, 22, 22, 22] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087930 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 38, 38, 38, 22, 18, 15, 3, 15, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 38, 38, 18, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 38 rigid atoms, others: [39, 40, 41, 42, 43, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 37 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087930 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087930/1 /scratch/stefan/7774412/working/building/REAL300004087930 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1185) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1185 `/scratch/stefan/7774412/working/3D/1185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1) `REAL300004087930.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087930 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 164, 174, 174, 114, 38, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 114, 114, 114, 114, 164, 164, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3] 174 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42]) total number of confs: 499 number of broken/clashed sets: 173 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087930 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 66, 66, 114, 114, 114, 114, 114, 114, 114, 114, 132, 132, 132, 132, 132, 1, 2, 2, 2, 2, 2, 114, 114, 114, 114, 114, 114, 132, 132, 132, 132, 132] 174 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 376 number of broken/clashed sets: 173 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087930 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2OCCC[C@H]2C2=CC=CC=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 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, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 174, 174, 174, 132, 51, 10, 3, 10, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 174, 174, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1] 174 rigid atoms, others: [38, 39, 40, 41, 42, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 437 number of broken/clashed sets: 173 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087930 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087930 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087930/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087930/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087930 Building REAL300004087931 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087931' /scratch/stefan/7774412/working/building/REAL300004087931 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087931 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087931/0 /scratch/stefan/7774412/working/building/REAL300004087931 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1186) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1186 `/scratch/stefan/7774412/working/3D/1186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCCNS2(=O)=O)S1) `REAL300004087931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087931 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 21, 21, 21, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 85 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087931 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C)CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087931 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087931/1 /scratch/stefan/7774412/working/building/REAL300004087931 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1187) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1187 `/scratch/stefan/7774412/working/3D/1187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCCNS2(=O)=O)S1) `REAL300004087931.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087931/1/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: REAL300004087931 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 75, 75, 75, 58, 22, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 75, 75, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1] 75 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 191 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087931 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C)CCCNS2(=O)=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 8, 14, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 12, 36, 36, 58, 58, 58, 58, 58, 58, 58, 58, 1, 2, 2, 2, 3, 3, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58] 75 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087931 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087931 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087931/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087931/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087931 Building REAL300004087932 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087932' /scratch/stefan/7774412/working/building/REAL300004087932 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087932 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087932/0 /scratch/stefan/7774412/working/building/REAL300004087932 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1188) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1188 `/scratch/stefan/7774412/working/3D/1188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C2CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)CCC2=N1) `REAL300004087932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087932 none CCC1=NC=C2CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)CCC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [36, 20, 20, 20, 20, 20, 20, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 20, 36, 36, 36, 36, 36, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 20, 20, 20, 20] 65 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 168 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: REAL300004087932 none CCC1=NC=C2CC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)CCC2=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 13, 20, 20, 20, 37, 38, 38, 20, 20, 20, 1, 1, 1, 1, 8, 8, 8, 7, 7, 1, 1, 1, 1, 13, 37, 37, 20, 20, 20, 1, 1, 1, 1] 65 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 41, 42, 43, 40, 21, 22, 23, 24, 33, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087932 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087932 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087932/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087932 Building REAL300004087933 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087933' /scratch/stefan/7774412/working/building/REAL300004087933 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087933 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087933/0 /scratch/stefan/7774412/working/building/REAL300004087933 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1189) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1189 `/scratch/stefan/7774412/working/3D/1189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(Br)S2)S1) `REAL300004087933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087933 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(Br)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 15, 15, 15, 11, 11, 11, 10, 10, 6, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 11, 10, 10, 6, 6, 1, 1] 15 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087933 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC2=CC=C(Br)S2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 17, 14, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 2, 2, 2, 4, 11, 11, 11, 11, 11, 1, 2, 2, 2, 3, 3, 2, 2, 2, 4, 4, 11, 11] 15 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087933 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087933 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087933/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087933 Building REAL300004087934 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087934' /scratch/stefan/7774412/working/building/REAL300004087934 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087934 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087934/0 /scratch/stefan/7774412/working/building/REAL300004087934 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1190) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1190 `/scratch/stefan/7774412/working/3D/1190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCCO2)S1) `REAL300004087934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087934 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 22, 22, 12, 12, 11, 6, 11, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1] 22 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087934 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2COCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 9, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12] 22 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 19] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087934 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087934 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087934/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087934 Building REAL300004087935 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087935' /scratch/stefan/7774412/working/building/REAL300004087935 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087935 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087935/0 /scratch/stefan/7774412/working/building/REAL300004087935 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1191) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1191 `/scratch/stefan/7774412/working/3D/1191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087935 none COCCC(C)(C)CC(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 105, 103, 38, 10, 37, 37, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 131, 131, 131, 106, 106, 104, 104, 38, 38, 38, 38, 38, 38, 10, 10, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 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: 515 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087935 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087935 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087935/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087935 Building REAL300004087936 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087936' /scratch/stefan/7774412/working/building/REAL300004087936 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087936 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087936/0 /scratch/stefan/7774412/working/building/REAL300004087936 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1192) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1192 `/scratch/stefan/7774412/working/3D/1192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C)(C)C(C)(F)F)S1) `REAL300004087936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087936 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C)(C)C(C)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 15, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087936 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087936 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087936/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087936 Building REAL300004087937 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087937' /scratch/stefan/7774412/working/building/REAL300004087937 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087937 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087937/0 /scratch/stefan/7774412/working/building/REAL300004087937 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1193) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1193 `/scratch/stefan/7774412/working/3D/1193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2CC2CC2)S1) `REAL300004087937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087937 none CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 20, 20, 20, 20, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 39, 57, 57, 20, 20, 20, 20, 20, 20, 2, 2, 2, 2, 2, 2, 39, 39, 57, 57, 57, 57, 57] 85 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087937 none CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 12, 20, 20, 20, 35, 55, 55, 20, 20, 20, 1, 1, 5, 12, 12, 1, 2, 2, 2, 1, 1, 12, 35, 35, 20, 20, 20, 5, 5, 12, 12, 12, 12, 12] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 20, 21, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087937 none CC1=CC2=C(C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N2CC2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 12, 38, 38, 43, 57, 57, 57, 85, 85, 85, 57, 57, 57, 6, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 43, 85, 85, 57, 57, 57, 6, 6, 1, 1, 1, 1, 1] 85 rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 316 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087937 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087937 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087937/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087937 Building REAL300004087938 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087938' /scratch/stefan/7774412/working/building/REAL300004087938 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087938 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087938/0 /scratch/stefan/7774412/working/building/REAL300004087938 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1194) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1194 `/scratch/stefan/7774412/working/3D/1194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCC=CBr)S1) `REAL300004087938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087938 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCC=CBr)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 10, 14, 25, 25, 1, 2, 2, 2, 2, 2, 2, 10, 10, 14, 14, 25, 25] 33 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 17] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 116 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087938 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087938 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087938/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087938 Building REAL300004087939 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087939' /scratch/stefan/7774412/working/building/REAL300004087939 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087939 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087939/0 /scratch/stefan/7774412/working/building/REAL300004087939 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1195) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1195 `/scratch/stefan/7774412/working/3D/1195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=NN(C)C=C2)CC3)S1) `REAL300004087939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087939 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=NN(C)C=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 17, 17, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 8, 8, 8, 8, 14, 14, 6, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 1, 1] 24 rigid atoms, others: [32, 33, 34, 40, 41, 10, 43, 12, 13, 14, 15, 16, 22, 23, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087939 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=NN(C)C=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 8, 8] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087939 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=NN(C)C=C2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 8, 8, 5, 1, 1, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 24, 24, 24, 15, 13, 13, 9, 13, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 15, 15, 15, 15, 24, 24, 13, 9, 9, 9, 9, 2, 2, 2, 1, 1, 9, 9, 9, 9] 24 rigid atoms, others: [38, 39, 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, 40, 41, 42, 43]) total number of confs: 88 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087939 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087939 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087939/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087939 Building REAL300004087940 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087940' /scratch/stefan/7774412/working/building/REAL300004087940 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087940 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087940/0 /scratch/stefan/7774412/working/building/REAL300004087940 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1196) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1196 `/scratch/stefan/7774412/working/3D/1196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=NC(C)=C2)S1) `REAL300004087940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087940 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 23, 23, 23, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 23, 23, 8, 2, 2, 2, 1, 2, 2, 2, 1] 23 rigid atoms, others: [34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087940 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)C=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 11, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087940 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087940 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087940/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087940 Building REAL300004087941 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087941' /scratch/stefan/7774412/working/building/REAL300004087941 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087941 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087941/0 /scratch/stefan/7774412/working/building/REAL300004087941 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1197) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1197 `/scratch/stefan/7774412/working/3D/1197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC(C)=CC(F)=C2)S1) `REAL300004087941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087941 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC(C)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 165, 165, 165, 103, 81, 73, 13, 73, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 103, 165, 165, 81, 13, 13, 13, 13, 1, 2, 2, 2, 1, 1] 165 rigid atoms, others: [33, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087941 none CC1=C(CC(=O)[O-])N=C(NC(=O)C(C)C2=CC(C)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 103, 103, 103, 102, 103, 103, 103, 1, 2, 2, 2, 3, 3, 2, 24, 25, 25, 25, 103, 103, 103, 103, 102, 103] 165 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087941 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087941/1 /scratch/stefan/7774412/working/building/REAL300004087941 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1198) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1198 `/scratch/stefan/7774412/working/3D/1198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC(C)=CC(F)=C2)S1) `REAL300004087941.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087941/1/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: REAL300004087941 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC(C)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 201, 201, 201, 146, 67, 27, 11, 27, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 201, 201, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [32, 36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087941 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C(C)C2=CC(C)=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 5, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 36, 36, 75, 75, 146, 146, 146, 146, 146, 146, 146, 1, 2, 2, 2, 2, 2, 75, 75, 75, 75, 146, 146, 146, 146, 146, 146] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 423 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087941 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087941 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087941/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087941/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087941 Building REAL300004087942 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087942' /scratch/stefan/7774412/working/building/REAL300004087942 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087942 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087942/0 /scratch/stefan/7774412/working/building/REAL300004087942 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1199) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1199 `/scratch/stefan/7774412/working/3D/1199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=CC=C2F)C(F)F)S1) `REAL300004087942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087942 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=CC=C2F)C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 4] 4 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087942 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC(C2=CC=CC=C2F)C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 15, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 1, 2, 2, 2, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 4] 4 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 24, 28, 29] set([5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087942 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087942 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087942/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087942 Building REAL300004087943 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087943' /scratch/stefan/7774412/working/building/REAL300004087943 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087943 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087943/0 /scratch/stefan/7774412/working/building/REAL300004087943 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1200) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1200 `/scratch/stefan/7774412/working/3D/1200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=CC=NN32)S1) `REAL300004087943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087943 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 27, 27, 27, 16, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087943 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCCC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 1, 2, 2, 2, 2, 2, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087943 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087943/1 /scratch/stefan/7774412/working/building/REAL300004087943 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1201) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1201 `/scratch/stefan/7774412/working/3D/1201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=CC=NN32)S1) `REAL300004087943.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087943/1/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: REAL300004087943 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 46, 57, 57, 57, 46, 19, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087943 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2CCCC3=CC=NN32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 8, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 32, 32, 46, 46, 46, 46, 46, 46, 46, 46, 1, 2, 2, 2, 2, 2, 46, 46, 46, 46, 46, 46, 46, 46, 46] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087943 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087943 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087943/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087943/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087943 Building REAL300004087944 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087944' /scratch/stefan/7774412/working/building/REAL300004087944 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087944 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087944/0 /scratch/stefan/7774412/working/building/REAL300004087944 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1202) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1202 `/scratch/stefan/7774412/working/3D/1202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CN=C(C(F)(F)F)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087944 none COC1=CN=C(C(F)(F)F)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2] 25 rigid atoms, others: [14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 50 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087944 none COC1=CN=C(C(F)(F)F)C=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 5, 15, 15, 15, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 10, 12, 15, 15, 15, 25, 25, 25, 15, 15, 15, 3, 3, 3, 1, 1, 12, 25, 25, 15, 15, 15] 25 rigid atoms, others: [1, 2, 3, 4, 5, 6, 10, 11, 12, 28, 29] set([0, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087944 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087944 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087944/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087944 Building REAL300004087945 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087945' /scratch/stefan/7774412/working/building/REAL300004087945 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087945 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087945/0 /scratch/stefan/7774412/working/building/REAL300004087945 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1203) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1203 `/scratch/stefan/7774412/working/3D/1203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3CC3(F)F)=C2)S1) `REAL300004087945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087945 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3CC3(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 6, 6, 6, 1] 69 rigid atoms, others: [32, 36, 10, 12, 13, 14, 15, 16, 17, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35]) total number of confs: 115 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087945 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3CC3(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 8, 13, 13, 38, 38, 38, 38, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 11, 38, 38, 38, 13] 69 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087945 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC(C3CC3(F)F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 69, 69, 69, 38, 30, 26, 6, 26, 6, 5, 6, 6, 1, 1, 1, 1, 1, 1, 6, 38, 38, 38, 38, 69, 69, 30, 5, 6, 6, 1, 1, 1, 6] 69 rigid atoms, others: [33, 34, 35, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 276 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087945 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087945 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087945/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087945 Building REAL300004087946 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087946' /scratch/stefan/7774412/working/building/REAL300004087946 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087946 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087946/0 /scratch/stefan/7774412/working/building/REAL300004087946 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1204) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1204 `/scratch/stefan/7774412/working/3D/1204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3CCCC3=C2)S1) `REAL300004087946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087946 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3CCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087946 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C3CCCC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087946 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087946 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087946/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087946 Building REAL300004087947 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087947' /scratch/stefan/7774412/working/building/REAL300004087947 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087947 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087947/0 /scratch/stefan/7774412/working/building/REAL300004087947 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1205) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1205 `/scratch/stefan/7774412/working/3D/1205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=C2C(F)F)S1) `REAL300004087947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087947 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 65, 85, 85, 37, 37, 37, 35, 37, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 37, 37, 65, 65, 37, 35, 35, 1, 1, 1, 1, 8] 105 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 390 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: REAL300004087947 none CC1=C(CC(=O)[O-])N=C(NC(=O)COC2=CC=CC=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 4, 12, 37, 37, 12, 37, 37, 37, 87, 87, 1, 2, 2, 2, 3, 3, 2, 4, 4, 37, 37, 12, 37, 87] 105 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 361 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087947 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087947/1 /scratch/stefan/7774412/working/building/REAL300004087947 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1206) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1206 `/scratch/stefan/7774412/working/3D/1206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=C2C(F)F)S1) `REAL300004087947.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087947/1/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: REAL300004087947 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 199, 199, 199, 165, 95, 53, 17, 53, 5, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 165, 165, 165, 165, 199, 199, 17, 17, 1, 1, 1, 1, 6] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 564 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087947 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)COC2=CC=CC=C2C(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 15, 15, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 9, 25, 25, 43, 125, 165, 165, 125, 165, 165, 165, 182, 182, 1, 2, 2, 2, 2, 2, 43, 43, 165, 165, 125, 165, 182] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087947 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087947 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087947/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087947/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087947 Building REAL300004087948 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087948' /scratch/stefan/7774412/working/building/REAL300004087948 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087948 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087948/0 /scratch/stefan/7774412/working/building/REAL300004087948 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1207) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1207 `/scratch/stefan/7774412/working/3D/1207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)SC2=NC=C1) `REAL300004087948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087948 none CCOC1=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)SC2=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [61, 41, 15, 15, 15, 15, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 15, 14, 15, 61, 61, 61, 61, 61, 15, 2, 2, 2, 2, 2, 2, 15, 15] 69 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087948 none CCOC1=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)SC2=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 14, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [23, 7, 1, 1, 1, 1, 1, 1, 11, 11, 11, 15, 15, 15, 29, 43, 43, 15, 15, 15, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 1, 11, 29, 29, 15, 15, 15, 1, 1] 69 rigid atoms, others: [2, 3, 4, 5, 6, 7, 20, 21, 22, 23, 24, 38, 30, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087948 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087948 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087948/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087948 Building REAL300004087949 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087949' /scratch/stefan/7774412/working/building/REAL300004087949 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087949 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087949/0 /scratch/stefan/7774412/working/building/REAL300004087949 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1208) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1208 `/scratch/stefan/7774412/working/3D/1208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2OCCC2(C)C)S1) `REAL300004087949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087949 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2OCCC2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 12, 12, 12, 7, 6, 6, 3, 6, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 6, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 12 rigid atoms, others: [32, 33, 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, 34, 35, 36, 37, 38, 39]) total number of confs: 62 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: REAL300004087949 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2OCCC2(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 12, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 6, 7, 7, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 12 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087949 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087949 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087949/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087949 Building REAL300004087950 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087950' /scratch/stefan/7774412/working/building/REAL300004087950 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087950 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087950/0 /scratch/stefan/7774412/working/building/REAL300004087950 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1209) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1209 `/scratch/stefan/7774412/working/3D/1209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)N=C2C)S1) `REAL300004087950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087950 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 27, 42, 42, 16, 12, 10, 1, 10, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 16, 16, 16, 16, 27, 27, 12, 1, 11, 11, 11, 11, 11, 2, 2, 2] 73 rigid atoms, others: [10, 12, 13, 14, 15, 16, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087950 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 16, 16, 5, 12, 47, 47, 16, 16, 16, 1, 2, 2, 2, 2, 2, 2, 16, 47, 47, 47, 47, 47, 16, 16, 16] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087950 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 73, 73, 73, 47, 38, 36, 5, 36, 1, 11, 11, 1, 1, 1, 1, 11, 11, 11, 47, 47, 47, 47, 73, 73, 38, 11, 1, 1, 1, 1, 1, 11, 11, 11] 73 rigid atoms, others: [32, 33, 34, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 283 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087950 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087950 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087950/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087950 Building REAL300004087951 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087951' /scratch/stefan/7774412/working/building/REAL300004087951 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087951 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087951/0 /scratch/stefan/7774412/working/building/REAL300004087951 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1210) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1210 `/scratch/stefan/7774412/working/3D/1210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1) `REAL300004087951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087951 none CCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 6, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 12, 12, 29, 29, 29, 29, 29, 12, 2, 2, 2, 2, 2, 2, 12, 12, 12] 49 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087951 none CCC1=NC=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 23, 27, 27, 12, 12, 12, 1, 1, 1, 8, 8, 8, 8, 8, 1, 8, 23, 23, 12, 12, 12, 2, 2, 2] 49 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087951 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087951 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087951/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087951 Building REAL300004087952 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087952' /scratch/stefan/7774412/working/building/REAL300004087952 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087952 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087952/0 /scratch/stefan/7774412/working/building/REAL300004087952 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1211) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1211 `/scratch/stefan/7774412/working/3D/1211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2C)S1) `REAL300004087952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087952 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 9, 17, 27, 27, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 1, 9, 9, 9, 9, 17, 17, 9, 1, 10, 11, 11, 10, 11, 10, 11, 11, 11, 2, 2, 2] 73 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087952 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 3, 8, 37, 37, 37, 37, 37, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9, 9] 73 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087952 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=C(C3CCOCC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 37, 73, 73, 73, 37, 37, 37, 8, 37, 2, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 37, 37, 37, 37, 73, 73, 37, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11] 73 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44]) total number of confs: 321 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087952 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087952 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087952/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087952 Building REAL300004087953 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087953' /scratch/stefan/7774412/working/building/REAL300004087953 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087953 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087953/0 /scratch/stefan/7774412/working/building/REAL300004087953 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1212) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1212 `/scratch/stefan/7774412/working/3D/1212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CC2C2C3C2(F)F)S1) `REAL300004087953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087953 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CC2C2C3C2(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 8, 8, 8, 14, 14, 14, 8, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 14, 14, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087953 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CC3CC2C2C3C2(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087953 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087953 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087953/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087953 Building REAL300004087954 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087954' /scratch/stefan/7774412/working/building/REAL300004087954 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087954 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087954/0 /scratch/stefan/7774412/working/building/REAL300004087954 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1213) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1213 `/scratch/stefan/7774412/working/3D/1213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CN=CS2)CC3)S1) `REAL300004087954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087954 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CN=CS2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 14, 15, 15, 8, 7, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 8, 8, 8, 8, 14, 14, 7, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 34, 35]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087954 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CN=CS2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 8, 8, 8, 8, 16, 16, 16, 16, 8, 8, 1, 2, 2, 2, 2, 2, 3, 8, 8, 8, 8, 16, 16, 8, 8, 8, 8] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087954 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2C3CC2(C2=CN=CS2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 23, 23, 23, 16, 15, 13, 5, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 16, 16, 16, 16, 23, 23, 15, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5] 23 rigid atoms, others: [34, 35, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087954 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087954 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087954/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087954 Building REAL300004087955 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087955' /scratch/stefan/7774412/working/building/REAL300004087955 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087955 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087955/0 /scratch/stefan/7774412/working/building/REAL300004087955 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1214) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1214 `/scratch/stefan/7774412/working/3D/1214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3(CC2)COCCO3)S1) `REAL300004087955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087955 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3(CC2)COCCO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 26, 26, 26, 14, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087955 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2CCC3(CC2)COCCO3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 26 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087955 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087955 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087955/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087955 Building REAL300004087956 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087956' /scratch/stefan/7774412/working/building/REAL300004087956 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087956 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087956/0 /scratch/stefan/7774412/working/building/REAL300004087956 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1215) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1215 `/scratch/stefan/7774412/working/3D/1215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CS2)CC3)S1) `REAL300004087956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087956 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CS2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 15, 15, 26, 36, 36, 15, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 15, 15, 15, 15, 26, 26, 11, 1, 1, 13, 13, 13, 1, 1, 1, 1] 62 rigid atoms, others: [32, 33, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36]) total number of confs: 150 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087956 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CS2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 4, 4, 15, 15, 15, 15, 15, 15, 38, 38, 38, 38, 15, 15, 1, 2, 2, 2, 2, 2, 3, 15, 15, 38, 38, 38, 15, 15, 15, 15] 62 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087956 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2[C@H]3C[C@]2(C2=CC=CS2)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 1, 14, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 62, 62, 62, 38, 34, 31, 13, 31, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 38, 38, 38, 38, 62, 62, 34, 13, 13, 1, 1, 1, 13, 13, 13, 13] 62 rigid atoms, others: [34, 35, 36, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40]) total number of confs: 234 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087956 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087956 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087956/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087956 Building REAL300004087957 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087957' /scratch/stefan/7774412/working/building/REAL300004087957 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087957 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087957/0 /scratch/stefan/7774412/working/building/REAL300004087957 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1216) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1216 `/scratch/stefan/7774412/working/3D/1216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCNS(=O)(=O)C3=C2)S1) `REAL300004087957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087957 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCNS(=O)(=O)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 8, 14, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 13, 13, 13, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 13, 13, 7, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087957 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NN3CCNS(=O)(=O)C3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 5, 5, 8, 14, 11, 11, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087957 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087957 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087957/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087957 Building REAL300004087958 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087958' /scratch/stefan/7774412/working/building/REAL300004087958 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087958 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087958/0 /scratch/stefan/7774412/working/building/REAL300004087958 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1217) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1217 `/scratch/stefan/7774412/working/3D/1217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=CC=C2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087958 none CC1=NN(C2=CC=CC=C2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 9, 9, 3, 3, 3, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 5, 5, 3, 3, 3, 8, 8] 15 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30, 31] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087958 none CC1=NN(C2=CC=CC=C2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 4, 8, 8, 8, 13, 13, 13, 13, 13, 13, 15, 15, 15, 13, 13, 13, 1, 1, 2, 2, 2, 8, 8, 8, 8, 13, 15, 15, 13, 13, 13, 1, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 38, 39, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087958 none CC1=NN(C2=CC=CC=C2C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 13, 13, 13, 13, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 13, 13] 15 rigid atoms, others: [12, 13, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 45 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087958 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087958 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087958/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087958 Building REAL300004087959 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087959' /scratch/stefan/7774412/working/building/REAL300004087959 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087959 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087959/0 /scratch/stefan/7774412/working/building/REAL300004087959 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1218) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1218 `/scratch/stefan/7774412/working/3D/1218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=CN=C2C)S1) `REAL300004087959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087959 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=CN=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 7, 7, 7, 4, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 3, 2, 2, 2, 1, 2, 2, 2] 7 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087959 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=CN=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 1, 8, 1, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 7 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087959 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087959 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087959/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087959 Building REAL300004087960 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087960' /scratch/stefan/7774412/working/building/REAL300004087960 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087960 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087960/0 /scratch/stefan/7774412/working/building/REAL300004087960 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1219) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1219 `/scratch/stefan/7774412/working/3D/1219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1) `REAL300004087960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087960 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 41, 51, 51, 22, 12, 12, 1, 12, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 22, 22, 22, 22, 41, 41, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [34, 35, 36, 37, 38, 39, 10, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 204 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087960 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 3, 3, 3, 22, 51, 51, 51, 51, 51, 51, 51, 22, 22, 22, 1, 2, 2, 2, 2, 2, 3, 51, 51, 51, 22, 22, 22, 22, 22, 22] 84 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 125 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087960 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 84, 84, 84, 51, 29, 29, 5, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 51, 51, 51, 51, 84, 84, 29, 1, 1, 1, 5, 5, 5, 5, 5, 5] 84 rigid atoms, others: [32, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39]) total number of confs: 309 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087960 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087960/1 /scratch/stefan/7774412/working/building/REAL300004087960 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1220) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1220 `/scratch/stefan/7774412/working/3D/1220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1) `REAL300004087960.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087960/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087960 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 135, 141, 141, 103, 48, 11, 1, 11, 1, 1, 5, 5, 5, 4, 5, 5, 5, 1, 1, 1, 103, 103, 103, 103, 135, 135, 5, 5, 5, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 10, 12, 13, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087960 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 13, 31, 31, 103, 157, 157, 157, 157, 157, 157, 157, 103, 103, 103, 1, 2, 2, 2, 2, 2, 157, 157, 157, 103, 103, 103, 103, 103, 103] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087960 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3=C(F)C=CC=C3Cl)CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 1, 1, 15, 1, 1, 1, 1, 16, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 201, 201, 201, 157, 81, 24, 5, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 157, 157, 157, 157, 201, 201, 1, 1, 1, 5, 5, 5, 5, 5, 5] 201 rigid atoms, others: [32, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38]) total number of confs: 505 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087960 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087960 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087960/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087960/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087960 Building REAL300004087961 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087961' /scratch/stefan/7774412/working/building/REAL300004087961 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087961 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087961/0 /scratch/stefan/7774412/working/building/REAL300004087961 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1221) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1221 `/scratch/stefan/7774412/working/3D/1221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3C[C@@]2(C2=CC=NN2C)CC3)S1) `REAL300004087961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087961 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3C[C@@]2(C2=CC=NN2C)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 8, 8, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 13, 15, 15, 7, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 13, 13, 5, 1, 1, 8, 8, 8, 8, 8, 1, 1, 1, 1] 24 rigid atoms, others: [33, 34, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 18, 24, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39]) total number of confs: 69 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: REAL300004087961 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3C[C@@]2(C2=CC=NN2C)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 8, 8, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 7, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 7, 13, 13, 13, 13, 13, 7, 7, 7, 7] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 26] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 52 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087961 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@H]2[C@@H]3C[C@@]2(C2=CC=NN2C)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 1, 1, 1, 8, 8, 5, 5, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 24, 24, 24, 13, 11, 10, 8, 10, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 24, 24, 11, 8, 8, 1, 1, 2, 2, 2, 8, 8, 8, 8] 24 rigid atoms, others: [35, 36, 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, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087961 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087961 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087961/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087961 Building REAL300004087962 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087962' /scratch/stefan/7774412/working/building/REAL300004087962 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087962 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087962/0 /scratch/stefan/7774412/working/building/REAL300004087962 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1222) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1222 `/scratch/stefan/7774412/working/3D/1222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC32CCC2)S1) `REAL300004087962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087962 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC32CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 5, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 33, 32, 22, 23, 24, 25, 26, 27, 28, 31]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087962 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC32CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087962 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087962/1 /scratch/stefan/7774412/working/building/REAL300004087962 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1223) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1223 `/scratch/stefan/7774412/working/3D/1223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC32CCC2)S1) `REAL300004087962.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087962/1/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: REAL300004087962 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC32CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [138, 138, 138, 138, 201, 201, 201, 138, 36, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138, 138, 138, 138, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 32, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 563 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087962 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC32CCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 58, 58, 138, 138, 138, 138, 138, 138, 138, 138, 138, 1, 2, 2, 2, 2, 2, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087962 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087962 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087962/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087962/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087962 Building REAL300004087963 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087963' /scratch/stefan/7774412/working/building/REAL300004087963 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087963 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087963/0 /scratch/stefan/7774412/working/building/REAL300004087963 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1224) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1224 `/scratch/stefan/7774412/working/3D/1224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC32CCOCC2)S1) `REAL300004087963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087963 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC32CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 17, 17, 17, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 17, 5, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 35, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087963 none CC1=C(CC(=O)[O-])N=C(NC(=O)C23CC(C)(C2)OC32CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087963 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087963/1 /scratch/stefan/7774412/working/building/REAL300004087963 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1225) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1225 `/scratch/stefan/7774412/working/3D/1225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC32CCOCC2)S1) `REAL300004087963.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087963/1/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: REAL300004087963 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC32CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 143, 201, 201, 201, 143, 34, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 34, 33, 32, 24, 25, 26, 27, 28, 29]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087963 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C23CC(C)(C2)OC32CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 57, 57, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 1, 2, 2, 2, 2, 2, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143, 143] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087963 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087963 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087963/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087963/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087963 Building REAL300004087964 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087964' /scratch/stefan/7774412/working/building/REAL300004087964 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087964 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087964/0 /scratch/stefan/7774412/working/building/REAL300004087964 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1226) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1226 `/scratch/stefan/7774412/working/3D/1226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H]3[C@@H](C2)C3(F)F)S1) `REAL300004087964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087964 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H]3[C@@H](C2)C3(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 21, 21, 21, 10, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 21, 21, 7, 1, 1, 1, 1, 1, 1] 21 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 92 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087964 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CC[C@H]3[C@@H](C2)C3(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 7, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 5, 5, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 3, 3, 2, 10, 10, 10, 10, 10, 10] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087964 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087964 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087964/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087964 Building REAL300004087965 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087965' /scratch/stefan/7774412/working/building/REAL300004087965 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087965 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087965/0 /scratch/stefan/7774412/working/building/REAL300004087965 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1227) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1227 `/scratch/stefan/7774412/working/3D/1227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C)=NC(C)=C2)S1) `REAL300004087965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087965 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C)=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 20, 21, 21, 12, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 20, 20, 9, 2, 2, 2, 2, 2, 2, 1] 21 rigid atoms, others: [33, 10, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087965 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NC(C)=NC(C)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 1, 5, 8, 1, 5, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 12] 21 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087965 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087965 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087965/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087965 Building REAL300004087966 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087966' /scratch/stefan/7774412/working/building/REAL300004087966 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087966 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087966/0 /scratch/stefan/7774412/working/building/REAL300004087966 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1228) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1228 `/scratch/stefan/7774412/working/3D/1228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC3=CC=C(F)C=C32)S1) `REAL300004087966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087966 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC3=CC=C(F)C=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 23, 23, 12, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 22, 22, 11, 1, 1, 1, 1] 23 rigid atoms, others: [32, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 99 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087966 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC3=CC=C(F)C=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087966 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087966 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087966/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087966 Building REAL300004087967 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087967' /scratch/stefan/7774412/working/building/REAL300004087967 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087967 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087967/0 /scratch/stefan/7774412/working/building/REAL300004087967 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1229) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1229 `/scratch/stefan/7774412/working/3D/1229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(C)C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1) `REAL300004087967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087967 none CC1=COC(C(C)C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 22, 21, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 20, 20, 20, 19, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 2, 2, 2] 39 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 80 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: REAL300004087967 none CC1=COC(C(C)C)=C1C(=O)NC1=NC(CC(=O)[O-])=C(C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 5, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 13, 20, 20, 20, 37, 39, 39, 19, 19, 19, 2, 2, 2, 1, 2, 2, 2, 2, 3, 3, 3, 13, 37, 37, 20, 20, 20] 39 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 25] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087967 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087967 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087967/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087967 Building REAL300004087968 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087968' /scratch/stefan/7774412/working/building/REAL300004087968 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087968 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087968/0 /scratch/stefan/7774412/working/building/REAL300004087968 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1230) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1230 `/scratch/stefan/7774412/working/3D/1230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C23CC(CC2)C3C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087968 none COC1=CC=C(C23CC(CC2)C3C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 9, 9, 9, 17, 27, 27, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 9, 9, 9, 7, 7] 29 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 39, 38, 37] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 131 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087968 none COC1=CC=C(C23CC(CC2)C3C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 15, 15, 17, 17, 17, 29, 29, 29, 17, 17, 17, 1, 1, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 15, 29, 29, 17, 17, 17, 1, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 46, 47, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087968 none COC1=CC=C(C23CC(CC2)C3C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [17, 16, 9, 17, 17, 9, 9, 9, 9, 9, 9, 4, 3, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 9, 3, 2, 2, 1, 1, 1, 17, 17] 29 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47]) total number of confs: 90 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087968 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087968 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087968/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087968 Building REAL300004087969 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087969' /scratch/stefan/7774412/working/building/REAL300004087969 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087969 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087969/0 /scratch/stefan/7774412/working/building/REAL300004087969 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1231) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1231 `/scratch/stefan/7774412/working/3D/1231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CCOCC2)S1) `REAL300004087969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087969 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 9, 10, 10, 5, 3, 3, 1, 3, 1, 1, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [45, 40, 41, 10, 43, 12, 13, 46, 44, 19, 20, 21, 22, 23, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 53 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087969 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 3, 3, 5, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 1, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5] 16 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 49 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087969 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCOCC3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 16, 16, 16, 9, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 9, 9, 9, 9, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 61 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087969 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087969/1 /scratch/stefan/7774412/working/building/REAL300004087969 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1232) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1232 `/scratch/stefan/7774412/working/3D/1232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CCOCC2)S1) `REAL300004087969.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087969 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 65, 65, 65, 51, 15, 3, 1, 3, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 51, 51, 51, 51, 65, 65, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1] 67 rigid atoms, others: [45, 39, 40, 41, 10, 43, 12, 13, 46, 44, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087969 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 33, 33, 51, 53, 53, 53, 53, 53, 51, 51, 51, 51, 51, 1, 2, 2, 2, 2, 2, 53, 53, 53, 53, 53, 53, 53, 53, 53, 51, 51, 51, 51, 51, 51, 51, 51] 67 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087969 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCOCC3)CCOCC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 67, 67, 67, 53, 19, 7, 5, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 53, 53, 53, 53, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5] 67 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 163 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087969 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087969 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087969/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087969/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087969 Building REAL300004087970 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087970' /scratch/stefan/7774412/working/building/REAL300004087970 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087970 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087970/0 /scratch/stefan/7774412/working/building/REAL300004087970 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1233) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1233 `/scratch/stefan/7774412/working/3D/1233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2(F)F)S1) `REAL300004087970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087970 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 28, 30, 30, 17, 14, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 28, 28, 14, 1, 1, 1, 1, 6, 6, 6] 49 rigid atoms, others: [32, 33, 10, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 129 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087970 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 17, 17, 6, 17, 17, 17, 32, 32, 32, 32, 1, 2, 2, 2, 2, 2, 2, 17, 17, 6, 17, 32, 32, 32] 49 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 115 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087970 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=CC=C2C2CC2(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 49, 49, 49, 32, 29, 23, 6, 23, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 49, 49, 29, 6, 6, 6, 6, 1, 1, 1] 49 rigid atoms, others: [34, 35, 36, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 183 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087970 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087970 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087970/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087970 Building REAL300004087971 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087971' /scratch/stefan/7774412/working/building/REAL300004087971 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087971 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087971/0 /scratch/stefan/7774412/working/building/REAL300004087971 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1234) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1234 `/scratch/stefan/7774412/working/3D/1234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2CC2)S1) `REAL300004087971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087971 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 46, 57, 57, 24, 14, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 9, 24, 24, 24, 24, 46, 46, 14, 1, 9, 9, 9, 9, 9] 78 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087971 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 24, 24, 24, 24, 24, 48, 48, 1, 2, 2, 2, 2, 2, 2, 24, 48, 48, 48, 48, 48] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087971 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN=NN2C2CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 8, 8, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 78, 78, 78, 48, 34, 29, 9, 29, 9, 9, 9, 9, 1, 1, 1, 1, 48, 48, 48, 48, 78, 78, 34, 9, 1, 1, 1, 1, 1] 78 rigid atoms, others: [32, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 290 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087971 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087971 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087971/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087971 Building REAL300004087972 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087972' /scratch/stefan/7774412/working/building/REAL300004087972 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087972 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087972/0 /scratch/stefan/7774412/working/building/REAL300004087972 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1235) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1235 `/scratch/stefan/7774412/working/3D/1235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NN(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1Cl) `REAL300004087972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087972 none CCC1=NN(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [33, 15, 15, 15, 15, 15, 4, 2, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 15, 15, 33, 33, 33, 33, 33, 15, 15, 15, 2, 2, 2, 2, 2, 2] 55 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087972 none CCC1=NN(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 9, 15, 15, 15, 27, 35, 35, 15, 15, 15, 1, 1, 3, 3, 3, 3, 3, 2, 2, 2, 9, 27, 27, 15, 15, 15] 55 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087972 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087972 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087972/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087972 Building REAL300004087973 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087973' /scratch/stefan/7774412/working/building/REAL300004087973 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087973 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087973/0 /scratch/stefan/7774412/working/building/REAL300004087973 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1236) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1236 `/scratch/stefan/7774412/working/3D/1236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CSC2=CC=CC(F)=C2)S1) `REAL300004087973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087973 none CC1=C(CC(=O)[O-])N=C(NC(=O)CSC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 55, 55, 55, 35, 35, 34, 32, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 55, 55, 35, 32, 32, 1, 1, 1, 1] 55 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 235 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087973 none CC1=C(CC(=O)[O-])N=C(NC(=O)CSC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 4, 10, 35, 35, 35, 35, 35, 35, 1, 2, 2, 2, 3, 3, 2, 4, 4, 35, 35, 35, 35] 55 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087973 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087973/1 /scratch/stefan/7774412/working/building/REAL300004087973 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1237) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1237 `/scratch/stefan/7774412/working/3D/1237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSC2=CC=CC(F)=C2)S1) `REAL300004087973.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087973/1/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: REAL300004087973 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [175, 175, 175, 175, 201, 201, 201, 175, 122, 84, 33, 84, 8, 1, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 201, 201, 33, 33, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 550 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087973 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSC2=CC=CC(F)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 15, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 12, 35, 35, 69, 125, 175, 175, 175, 175, 175, 175, 1, 2, 2, 2, 2, 2, 69, 69, 175, 175, 175, 175] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 421 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087973 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087973 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087973/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087973/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087973 Building REAL300004087974 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087974' /scratch/stefan/7774412/working/building/REAL300004087974 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087974 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087974/0 /scratch/stefan/7774412/working/building/REAL300004087974 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1238) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1238 `/scratch/stefan/7774412/working/3D/1238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C(Br)O3)N2)S1) `REAL300004087974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087974 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C(Br)O3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 25, 25, 25, 15, 11, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 25, 25, 11, 1, 1, 1] 25 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 95 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087974 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=C(C=C(Br)O3)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'O.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 17, 12, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 15, 15, 15, 15, 14, 14, 15, 15, 1, 2, 2, 2, 2, 2, 2, 15, 15, 15] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087974 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087974 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087974/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087974 Building REAL300004087975 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087975' /scratch/stefan/7774412/working/building/REAL300004087975 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087975 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087975/0 /scratch/stefan/7774412/working/building/REAL300004087975 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1239) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1239 `/scratch/stefan/7774412/working/3D/1239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=C(C3CC3)N=C2C)S1) `REAL300004087975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087975 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=C(C3CC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 8, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 11, 18, 18, 6, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 5, 2, 2, 2, 11, 11, 11, 11, 11, 2, 2, 2] 24 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087975 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=C(C3CC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 8, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 6, 6, 6, 4, 4, 15, 15, 6, 6, 6, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 15, 15, 15, 15, 15, 6, 6, 6] 24 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087975 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C)N=C(C3CC3)N=C2C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 8, 1, 5, 5, 5, 8, 1, 5, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 24, 24, 24, 15, 13, 10, 1, 10, 1, 11, 11, 11, 1, 1, 1, 1, 11, 11, 11, 15, 15, 15, 15, 24, 24, 11, 11, 11, 11, 1, 1, 1, 1, 1, 11, 11, 11] 24 rigid atoms, others: [33, 34, 35, 36, 37, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087975 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087975 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087975/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087975 Building REAL300004087976 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087976' /scratch/stefan/7774412/working/building/REAL300004087976 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087976 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087976/0 /scratch/stefan/7774412/working/building/REAL300004087976 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1240) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1240 `/scratch/stefan/7774412/working/3D/1240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1) `REAL300004087976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087976 none CCC1=NC(C)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 4, 6, 6, 6, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 6, 6, 6, 2, 2, 2, 2, 2, 2, 6, 6, 6] 19 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087976 none CCC1=NC(C)=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 6, 6, 6, 11, 11, 11, 6, 6, 6, 1, 1, 1, 7, 7, 7, 6, 6, 2, 2, 2, 5, 11, 11, 6, 6, 6, 2, 2, 2] 19 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 20, 21, 22] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087976 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087976 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087976/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087976 Building REAL300004087977 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087977' /scratch/stefan/7774412/working/building/REAL300004087977 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087977 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087977/0 /scratch/stefan/7774412/working/building/REAL300004087977 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1241) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1241 `/scratch/stefan/7774412/working/3D/1241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)OC=C2C(F)(F)F)S1) `REAL300004087977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087977 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)OC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 15, 15, 27, 27, 27, 14, 10, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 14, 15, 15, 15, 27, 27, 10, 1, 1, 1, 1, 2, 2, 2, 1] 27 rigid atoms, others: [32, 33, 34, 38, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087977 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=C(C(C)C)OC=C2C(F)(F)F)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'F', 'F', 'F', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 5, 5, 5, 12, 1, 1, 5, 15, 15, 15, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 14, 14, 15, 14, 14, 14, 14, 14, 15, 15, 15, 1, 2, 2, 2, 2, 2, 2, 14, 15, 15, 15, 15, 15, 15, 14] 27 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087977 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087977 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087977/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087977 Building REAL300004087978 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087978' /scratch/stefan/7774412/working/building/REAL300004087978 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087978 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087978/0 /scratch/stefan/7774412/working/building/REAL300004087978 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1242) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1242 `/scratch/stefan/7774412/working/3D/1242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C(F)(F)F)=CO1) `REAL300004087978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087978 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C(F)(F)F)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 18, 3, 2, 3, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 18, 18, 19, 19, 19, 18, 18, 33, 33, 33, 33, 33, 2, 2, 2, 2, 2, 2, 18] 54 rigid atoms, others: [6, 7, 8, 9, 10, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 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: REAL300004087978 none CCC1=C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C(C(F)(F)F)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 5, 15, 15, 15, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 10, 10, 12, 18, 18, 18, 34, 38, 38, 18, 18, 18, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 12, 34, 34, 19, 19, 19, 1] 54 rigid atoms, others: [1, 2, 3, 4, 17, 18, 35, 22, 23] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 180 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087978 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087978 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087978/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087978 Building REAL300004087979 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087979' /scratch/stefan/7774412/working/building/REAL300004087979 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087979 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087979/0 /scratch/stefan/7774412/working/building/REAL300004087979 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1243) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1243 `/scratch/stefan/7774412/working/3D/1243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NNC2=O)S1) `REAL300004087979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087979 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 11, 19, 19, 7, 6, 6, 1, 6, 1, 1, 1, 1, 8, 8, 1, 1, 1, 1, 7, 7, 7, 7, 11, 11, 6, 1, 8, 8, 8, 8, 8, 1] 28 rigid atoms, others: [35, 10, 12, 13, 14, 15, 18, 19, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087979 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 4, 4, 7, 7, 7, 20, 20, 7, 7, 7, 7, 1, 2, 2, 2, 2, 2, 2, 7, 20, 20, 20, 20, 20, 7] 28 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087979 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC(C3CC3)=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 28, 28, 28, 20, 17, 17, 8, 17, 8, 8, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 20, 20, 28, 28, 17, 8, 1, 1, 1, 1, 1, 8] 28 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) total number of confs: 93 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087979 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087979/1 /scratch/stefan/7774412/working/building/REAL300004087979 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1244) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1244 `/scratch/stefan/7774412/working/3D/1244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CC(C3CC3)=NNC2=O)S1) `REAL300004087979.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087979/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087979 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CC(C3CC3)=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 123, 169, 169, 105, 33, 10, 1, 10, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 105, 105, 105, 105, 123, 123, 1, 11, 11, 11, 11, 11, 1] 201 rigid atoms, others: [34, 10, 12, 13, 14, 15, 18, 19, 20, 21, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087979 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CC(C3CC3)=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 51, 51, 105, 105, 105, 195, 195, 105, 105, 105, 105, 1, 2, 2, 2, 2, 2, 105, 195, 195, 195, 195, 195, 105] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087979 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2=CC(C3CC3)=NNC2=O)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.am', 'C.2', 'O.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 8, 1, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 195, 201, 201, 201, 195, 116, 62, 11, 62, 11, 11, 1, 1, 1, 1, 11, 11, 11, 11, 195, 195, 195, 195, 201, 201, 11, 1, 1, 1, 1, 1, 11] 201 rigid atoms, others: [32, 33, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087979 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087979 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087979/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087979/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087979 Building REAL300004087980 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087980' /scratch/stefan/7774412/working/building/REAL300004087980 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087980 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087980/0 /scratch/stefan/7774412/working/building/REAL300004087980 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1245) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1245 `/scratch/stefan/7774412/working/3D/1245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CC2)S1) `REAL300004087980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087980 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 25, 27, 27, 13, 8, 7, 1, 7, 1, 1, 8, 8, 8, 8, 8, 1, 1, 13, 13, 13, 13, 25, 25, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1] 52 rigid atoms, others: [37, 38, 39, 40, 10, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 125 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087980 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 3, 4, 4, 13, 27, 27, 27, 27, 27, 13, 13, 1, 2, 2, 2, 2, 2, 3, 27, 27, 27, 27, 27, 27, 27, 27, 27, 13, 13, 13, 13] 52 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087980 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(C3CCCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 52, 52, 52, 27, 19, 17, 8, 17, 1, 1, 1, 1, 1, 1, 1, 8, 8, 27, 27, 27, 27, 52, 52, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 52 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 219 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087980 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087980/1 /scratch/stefan/7774412/working/building/REAL300004087980 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1246) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1246 `/scratch/stefan/7774412/working/3D/1246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CC2)S1) `REAL300004087980.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087980 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 199, 200, 200, 136, 40, 7, 1, 7, 1, 1, 6, 6, 6, 6, 6, 1, 1, 136, 136, 136, 136, 199, 199, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 10, 12, 13, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 571 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087980 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 75, 75, 136, 144, 144, 144, 144, 144, 136, 136, 1, 2, 2, 2, 2, 2, 144, 144, 144, 144, 144, 144, 144, 144, 144, 136, 136, 136, 136] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 406 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087980 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(C3CCCCO3)CC2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 144, 201, 201, 201, 144, 56, 15, 6, 15, 1, 1, 1, 1, 1, 1, 1, 6, 6, 144, 144, 144, 144, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39]) total number of confs: 550 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087980 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087980 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087980/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087980/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087980 Building REAL300004087981 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087981' /scratch/stefan/7774412/working/building/REAL300004087981 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087981 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087981/0 /scratch/stefan/7774412/working/building/REAL300004087981 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1247) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1247 `/scratch/stefan/7774412/working/3D/1247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1) `REAL300004087981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087981 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 20, 34, 34, 11, 7, 7, 1, 7, 1, 1, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 7, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [38, 39, 40, 41, 10, 43, 12, 13, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087981 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 2, 2, 11, 28, 28, 28, 28, 28, 28, 28, 11, 11, 11, 9, 1, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11] 47 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087981 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 47, 47, 47, 28, 21, 21, 8, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 28, 28, 28, 28, 47, 47, 21, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087981 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087981/1 /scratch/stefan/7774412/working/building/REAL300004087981 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1248) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1248 `/scratch/stefan/7774412/working/3D/1248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1) `REAL300004087981.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087981/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087981 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 144, 163, 163, 108, 31, 11, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 108, 108, 108, 108, 144, 144, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 12, 13, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 460 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087981 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 55, 55, 108, 164, 164, 164, 164, 164, 164, 164, 108, 108, 108, 108, 1, 2, 2, 2, 2, 2, 164, 164, 164, 164, 164, 164, 108, 108, 108, 108, 108, 108] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 25] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 605 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087981 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)C2(CC3=CC=C(F)C=C3)CCCO2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 201, 201, 201, 164, 65, 27, 7, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 164, 164, 164, 164, 201, 201, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42]) total number of confs: 475 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087981 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087981 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087981/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087981/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087981 Building REAL300004087982 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087982' /scratch/stefan/7774412/working/building/REAL300004087982 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087982 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087982/0 /scratch/stefan/7774412/working/building/REAL300004087982 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1249) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1249 `/scratch/stefan/7774412/working/3D/1249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC(C)=CC(C)=C3N2)S1) `REAL300004087982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087982 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC(C)=CC(C)=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 2, 2, 2, 1, 2, 2, 2, 1] 25 rigid atoms, others: [35, 39, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087982 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC3=CC(C)=CC(C)=C3N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 1, 5, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087982 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087982 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087982/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087982 Building REAL300004087983 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087983' /scratch/stefan/7774412/working/building/REAL300004087983 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087983 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087983/0 /scratch/stefan/7774412/working/building/REAL300004087983 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1250) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1250 `/scratch/stefan/7774412/working/3D/1250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC2=C(NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2)S1) `REAL300004087983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087983 none CC1=NC2=C(NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 12, 13, 13, 13, 12, 2, 2, 2, 2, 2, 2, 12] 23 rigid atoms, others: [9, 10, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087983 none CC1=NC2=C(NC(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 22, 23, 23, 12, 12, 12, 1, 1, 2, 2, 2, 1, 8, 22, 22, 13, 13, 13, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 20, 21, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087983 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087983 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087983/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087983 Building REAL300004087984 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087984' /scratch/stefan/7774412/working/building/REAL300004087984 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087984 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087984/0 /scratch/stefan/7774412/working/building/REAL300004087984 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1251) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1251 `/scratch/stefan/7774412/working/3D/1251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC3=C2COC3(C)C)S1) `REAL300004087984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087984 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC3=C2COC3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 13, 14, 14, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 11, 11, 11, 13, 13, 8, 1, 1, 1, 2, 2, 2, 2, 2, 2] 14 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087984 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC3=C2COC3(C)C)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 1, 5, 12, 5, 5, 5, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 11, 11, 11, 11, 11, 11] 14 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087984 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087984 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087984/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087984 Building REAL300004087985 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087985' /scratch/stefan/7774412/working/building/REAL300004087985 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087985 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087985/0 /scratch/stefan/7774412/working/building/REAL300004087985 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1252) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1252 `/scratch/stefan/7774412/working/3D/1252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CC=N2)S1) `REAL300004087985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087985 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 46, 46, 46, 24, 22, 19, 10, 21, 10, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 46, 46, 19, 10, 10, 1, 1, 1] 46 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 202 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087985 none CC1=C(CC(=O)[O-])N=C(NC(=O)C=CC2=CN=CC=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 3, 3, 11, 11, 24, 24, 23, 24, 24, 1, 2, 2, 2, 3, 3, 2, 11, 11, 24, 23, 24] 46 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 20] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087985 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087985 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087985/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087985 Building REAL300004087986 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087986' /scratch/stefan/7774412/working/building/REAL300004087986 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087986 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087986/0 /scratch/stefan/7774412/working/building/REAL300004087986 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1253) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1253 `/scratch/stefan/7774412/working/3D/1253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3CCOCC3)=C2)S1) `REAL300004087986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087986 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3CCOCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 14, 25, 32, 32, 14, 10, 10, 1, 10, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 1, 14, 15, 15, 15, 25, 25, 10, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 78 rigid atoms, others: [40, 10, 12, 13, 14, 15, 16, 22, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 155 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087986 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3CCOCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 14, 14, 14, 14, 48, 48, 48, 48, 48, 14, 1, 2, 2, 2, 2, 2, 2, 14, 48, 48, 48, 48, 48, 48, 48, 48, 48, 14] 78 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087986 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NNC(C3CCOCC3)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 8, 1, 5, 5, 5, 12, 5, 5, 1, 14, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 78, 78, 78, 48, 39, 39, 13, 39, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 13, 48, 48, 48, 48, 78, 78, 39, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40]) total number of confs: 288 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087986 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087986 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087986/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087986 Building REAL300004087987 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087987' /scratch/stefan/7774412/working/building/REAL300004087987 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087987 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087987/0 /scratch/stefan/7774412/working/building/REAL300004087987 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1254) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1254 `/scratch/stefan/7774412/working/3D/1254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCCC3)N=C2)S1) `REAL300004087987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087987 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 13, 21, 24, 24, 13, 9, 7, 1, 7, 1, 1, 1, 1, 10, 10, 10, 10, 1, 1, 13, 13, 13, 13, 21, 21, 9, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 79 rigid atoms, others: [39, 10, 12, 13, 14, 15, 20, 21, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 111 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087987 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 43, 43, 43, 43, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 43, 43, 43, 43, 43, 43, 43, 43, 43, 13] 79 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 124 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087987 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CN(C3CCCC3)N=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 5, 8, 1, 14, 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, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 79, 79, 79, 43, 27, 27, 10, 27, 10, 10, 1, 1, 1, 1, 1, 1, 10, 10, 43, 43, 43, 43, 79, 79, 27, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 79 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 303 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087987 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087987 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087987/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087987 Building REAL300004087988 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087988' /scratch/stefan/7774412/working/building/REAL300004087988 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087988 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087988/0 /scratch/stefan/7774412/working/building/REAL300004087988 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1255) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1255 `/scratch/stefan/7774412/working/3D/1255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC3=C2CC(F)(F)CC3)S1) `REAL300004087988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087988 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC3=C2CC(F)(F)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 15, 15, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 22, 23, 23, 12, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 13, 13, 13, 22, 22, 8, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087988 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=NOC3=C2CC(F)(F)CC3)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 8, 12, 1, 1, 5, 5, 15, 15, 5, 5, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 12, 12, 12, 12] 23 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087988 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087988 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087988/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087988 Building REAL300004087989 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087989' /scratch/stefan/7774412/working/building/REAL300004087989 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087989 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087989/0 /scratch/stefan/7774412/working/building/REAL300004087989 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1256) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1256 `/scratch/stefan/7774412/working/3D/1256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CC3=CC=CN=C32)S1) `REAL300004087989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087989 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CC3=CC=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 57, 57, 57, 40, 40, 38, 16, 38, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 57, 57, 40, 16, 16, 8, 8, 1, 1, 1, 1, 1] 57 rigid atoms, others: [34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 233 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087989 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CC3=CC=CN=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 12, 18, 40, 40, 40, 40, 40, 40, 40, 40, 1, 2, 2, 2, 2, 2, 2, 12, 12, 18, 18, 40, 34, 40, 40, 40] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 23] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087989 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087989 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087989/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087989 Building REAL300004087990 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087990' /scratch/stefan/7774412/working/building/REAL300004087990 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087990 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087990/0 /scratch/stefan/7774412/working/building/REAL300004087990 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1257) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1257 `/scratch/stefan/7774412/working/3D/1257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1) `REAL300004087990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087990 none CCCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [57, 48, 12, 12, 12, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 12, 12, 58, 58, 58, 57, 57, 48, 48, 2, 2, 2, 2, 2, 2, 12] 96 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087990 none CCCC1=NC(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 1, 1, 1, 1, 1, 9, 9, 9, 12, 12, 12, 24, 56, 56, 12, 12, 12, 1, 1, 18, 18, 18, 17, 17, 8, 8, 9, 24, 24, 13, 13, 13, 1] 96 rigid atoms, others: [2, 3, 4, 5, 6, 34, 19, 20] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087990 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087990 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087990/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087990 Building REAL300004087991 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087991' /scratch/stefan/7774412/working/building/REAL300004087991 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087991 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087991/0 /scratch/stefan/7774412/working/building/REAL300004087991 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1258) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1258 `/scratch/stefan/7774412/working/3D/1258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1Cl) `REAL300004087991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087991 none CC1=NN(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 4, 2, 4, 1, 1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 2, 2] 21 rigid atoms, others: [8, 9, 10, 11, 12, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087991 none CC1=NN(C)C(C(=O)NC2=NC(CC(=O)[O-])=C(C)S2)=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 16, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 21, 21, 11, 11, 11, 1, 1, 2, 2, 2, 2, 2, 2, 7, 21, 21, 11, 11, 11] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087991 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087991 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087991/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087991 Building REAL300004087992 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087992' /scratch/stefan/7774412/working/building/REAL300004087992 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087992 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087992/0 /scratch/stefan/7774412/working/building/REAL300004087992 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1259) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1259 `/scratch/stefan/7774412/working/3D/1259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)(C)C)N2)S1) `REAL300004087992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087992 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)(C)C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 23, 27, 27, 13, 9, 9, 1, 9, 1, 1, 1, 1, 1, 4, 4, 4, 1, 13, 13, 13, 13, 23, 23, 9, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 41 rigid atoms, others: [39, 10, 12, 13, 14, 15, 16, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087992 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C(C(C)(C)C)N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 23, 23, 23, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 13] 41 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087992 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087992 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087992/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087992 Building REAL300004087993 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087993' /scratch/stefan/7774412/working/building/REAL300004087993 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087993 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087993/0 /scratch/stefan/7774412/working/building/REAL300004087993 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1260) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1260 `/scratch/stefan/7774412/working/3D/1260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=C2N1) `REAL300004087993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087993 none COC1=CC=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 18, 18, 18, 3, 2, 3, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 18, 18, 18, 34, 34, 34, 18, 18, 18, 2, 2, 2, 2, 2, 2, 18] 37 rigid atoms, others: [10, 11, 12, 13, 14, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 79 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087993 none COC1=CC=C2C=C(C(=O)NC3=NC(CC(=O)[O-])=C(C)S3)N=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'N.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 15, 18, 18, 18, 28, 37, 37, 18, 18, 18, 1, 1, 1, 8, 8, 8, 1, 1, 1, 15, 28, 28, 19, 19, 19, 1] 37 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 36, 27, 28, 29] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 30, 31, 32, 33, 34, 35]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087993 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087993 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087993/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087993 Building REAL300004087994 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087994' /scratch/stefan/7774412/working/building/REAL300004087994 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087994 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087994/0 /scratch/stefan/7774412/working/building/REAL300004087994 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1261) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1261 `/scratch/stefan/7774412/working/3D/1261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC(C(C)(C)C)=N2)S1) `REAL300004087994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087994 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 12, 12, 12, 17, 21, 21, 12, 11, 9, 1, 9, 1, 1, 1, 1, 1, 4, 4, 4, 1, 12, 12, 12, 12, 17, 17, 11, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 29 rigid atoms, others: [10, 12, 13, 14, 15, 16, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 94 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087994 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CNC(C(C)(C)C)=N2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 12, 12, 12, 12, 19, 19, 19, 12, 1, 2, 2, 2, 2, 2, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19] 29 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087994 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087994 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087994/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087994 Building REAL300004087995 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087995' /scratch/stefan/7774412/working/building/REAL300004087995 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004087995 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087995/0 /scratch/stefan/7774412/working/building/REAL300004087995 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1262) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1262 `/scratch/stefan/7774412/working/3D/1262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC3=CC=CC=C32)S1) `REAL300004087995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087995 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 38, 38, 38, 24, 15, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 38, 38, 15, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [32, 33, 34, 35, 36, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 139 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: REAL300004087995 none CC1=C(CC(=O)[O-])N=C(NC(=O)[C@@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 2, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 2, 2, 2, 24, 24, 24, 24, 24, 24, 24, 24] 38 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 83 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087995 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004087995/1 /scratch/stefan/7774412/working/building/REAL300004087995 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1263) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1263 `/scratch/stefan/7774412/working/3D/1263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCC3=CC=CC=C32)S1) `REAL300004087995.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004087995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087995/1/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: REAL300004087995 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 156, 201, 201, 201, 156, 49, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 22, 23, 24, 25, 26, 27]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087995 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)[C@@H]2CCC3=CC=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 7, 7, 1, 1, 1, 13, 66, 66, 156, 156, 156, 156, 156, 156, 156, 156, 156, 1, 2, 2, 2, 2, 2, 156, 156, 156, 156, 156, 156, 156, 156] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087995 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087995 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004087995/1.* 0: /scratch/stefan/7774412/working/building/REAL300004087995/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087995 Building REAL300004087996 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087996' /scratch/stefan/7774412/working/building/REAL300004087996 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087996 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087996/0 /scratch/stefan/7774412/working/building/REAL300004087996 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1264) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1264 `/scratch/stefan/7774412/working/3D/1264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCOC3=C2)S1) `REAL300004087996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087996 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCOC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 25, 25, 25, 13, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 25, 25, 9, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [32, 33, 34, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087996 none CC1=C(CC(=O)[O-])N=C(NC(=O)C2=CC=C3CCOC3=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 12, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13] 25 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087996 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087996 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087996/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087996 Building REAL300004087997 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087997' /scratch/stefan/7774412/working/building/REAL300004087997 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087997 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087997/0 /scratch/stefan/7774412/working/building/REAL300004087997 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1265) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1265 `/scratch/stefan/7774412/working/3D/1265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CC2C[C@@H]3COC[C@H]23)S1) `REAL300004087997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087997 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2C[C@@H]3COC[C@H]23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 12, 5, 5, 7, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 13, 13, 13, 9, 9, 9, 5, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 13, 13, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087997 none CC1=C(CC(=O)[O-])N=C(NC(=O)CC2C[C@@H]3COC[C@H]23)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 5, 5, 7, 5, 12, 5, 5, 7, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 4, 4, 1, 1, 1, 3, 3, 2, 6, 9, 9, 9, 9, 9, 9, 9, 9, 1, 2, 2, 2, 2, 2, 3, 6, 6, 9, 9, 9, 9, 9, 9, 9] 13 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 22] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 56 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087997 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087997 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087997/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087997 Building REAL300004087998 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087998' /scratch/stefan/7774412/working/building/REAL300004087998 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087998 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087998/0 /scratch/stefan/7774412/working/building/REAL300004087998 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1266) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1266 `/scratch/stefan/7774412/working/3D/1266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CC3=CC(C)=CC=C32)S1) `REAL300004087998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087998 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CC3=CC(C)=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 61, 61, 61, 34, 34, 32, 12, 32, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 61, 61, 34, 12, 12, 6, 6, 1, 1, 1, 2, 2, 2, 1, 1] 61 rigid atoms, others: [35, 36, 37, 41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) 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: REAL300004087998 none CC1=C(CC(=O)[O-])N=C(NC(=O)CCN2C=CC3=CC(C)=CC=C32)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 5, 1, 1, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 5, 5, 1, 1, 1, 2, 2, 2, 12, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 2, 2, 2, 2, 2, 2, 12, 12, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34] 61 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 24] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087998 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087998 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087998/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087998 Building REAL300004087999 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004087999' /scratch/stefan/7774412/working/building/REAL300004087999 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004087999 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004087999/0 /scratch/stefan/7774412/working/building/REAL300004087999 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1267) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1267 `/scratch/stefan/7774412/working/3D/1267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(C)=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1) `REAL300004087999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004087999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004087999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087999 none COC1=CC=C(C(C)=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 6, 17, 17, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 3, 2, 2, 2, 2, 2, 17, 17] 20 rigid atoms, others: [11, 12, 13, 14, 15, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 85 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004087999 none COC1=CC=C(C(C)=CC(=O)NC2=NC(CC(=O)[O-])=C(C)S2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 1, 8, 1, 5, 1, 11, 11, 1, 5, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 17, 17, 17, 17, 17, 17, 20, 20, 20, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 17, 20, 20, 17, 17, 17, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 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]) total number of confs: 61 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004087999 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004087999 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 0: /scratch/stefan/7774412/working/building/REAL300004087999/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004087999 Building REAL300004088000 mkdir: created directory `/scratch/stefan/7774412/working/building/REAL300004088000' /scratch/stefan/7774412/working/building/REAL300004088000 /scratch/stefan/7774412/working /scratch/stefan/7774412 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004088000 mkdir: created directory `0' /scratch/stefan/7774412/working/building/REAL300004088000/0 /scratch/stefan/7774412/working/building/REAL300004088000 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 0 (index: 1268) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1268 `/scratch/stefan/7774412/working/3D/1268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C(NC(=O)CSC2=CC=CC(Cl)=C2)S1) `REAL300004088000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004088000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004088000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004088000 none CC1=C(CC(=O)[O-])N=C(NC(=O)CSC2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 57, 57, 57, 35, 35, 34, 32, 34, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 57, 57, 35, 32, 32, 1, 1, 1, 1] 57 rigid atoms, others: [32, 33, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 247 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004088000 none CC1=C(CC(=O)[O-])N=C(NC(=O)CSC2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 7, 7, 1, 1, 1, 2, 2, 2, 4, 10, 35, 35, 34, 35, 35, 35, 1, 2, 2, 2, 3, 3, 2, 4, 4, 35, 35, 35, 35] 57 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 85 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004088000 /scratch/stefan/7774412/working /scratch/stefan/7774412 mkdir: created directory `1' /scratch/stefan/7774412/working/building/REAL300004088000/1 /scratch/stefan/7774412/working/building/REAL300004088000 /scratch/stefan/7774412/working /scratch/stefan/7774412 Protomer 1 (index: 1269) Found valid previously generated 3D confromation in /scratch/stefan/7774412/working/3D/1269 `/scratch/stefan/7774412/working/3D/1269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSC2=CC=CC(Cl)=C2)S1) `REAL300004088000.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004088000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774412/working/building/REAL300004088000/1/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: REAL300004088000 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSC2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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: [171, 171, 171, 171, 201, 201, 201, 171, 116, 83, 31, 83, 8, 1, 1, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 201, 201, 31, 31, 1, 1, 1, 1] 201 rigid atoms, others: [32, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 572 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004088000 none CC1=C(CC(=O)[O-])N=C([N-]C(=O)CSC2=CC=CC(Cl)=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'N.2', 'C.2', 'O.2', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 11, 11, 8, 1, 8, 1, 11, 5, 14, 1, 1, 1, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 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, 2, 7, 7, 1, 1, 1, 12, 35, 35, 69, 122, 171, 161, 171, 171, 171, 171, 1, 2, 2, 2, 2, 2, 69, 69, 171, 171, 171, 171] 201 rigid atoms, others: [0, 1, 2, 3, 7, 8, 9, 21] set([4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 458 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774412/working/building/REAL300004088000 /scratch/stefan/7774412/working /scratch/stefan/7774412 Finished preparing REAL300004088000 Recording results /scratch/stefan/7774412/working /scratch/stefan/7774412 Appending to /scratch/stefan/7774412/finished/xaaaadj.* 1: /scratch/stefan/7774412/working/building/REAL300004088000/1.* 0: /scratch/stefan/7774412/working/building/REAL300004088000/0.* Removing working files in /scratch/stefan/7774412/working/building/REAL300004088000 /scratch/stefan/7774412 Compressing combined databse files /scratch/stefan/7774412/finished/xaaaadj.db2.gz /scratch/stefan/7774412/finished/xaaaadj.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7774412/finished) ======================================================= Finalizing... removed `/scratch/stefan/7774412/working/3D/1270' removed directory: `/scratch/stefan/7774412/working/3D' `/scratch/stefan/7774412/working/protonate' -> `/scratch/stefan/7774412/archive' `/scratch/stefan/7774412/working/input-smiles.ism' -> `/scratch/stefan/7774412/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7774412/working/building' rmdir: removing directory, `/scratch/stefan/7774412/working' ls: No match. ls: No match.