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/7901152/working' mkdir: created directory `/scratch/stefan/7901152/working/protonate' Storing results in /scratch/stefan/7901152/finished Working in /scratch/stefan/7901152/working /scratch/stefan/7901152/working /scratch/stefan/7901152 /scratch/stefan/7901152/working/protonate /scratch/stefan/7901152/working /scratch/stefan/7901152 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 99 protomers created Coalesing and merging protomers 91 protomers generated for 86 compounds Checking for new stereocenters and expanding 91 protomers after new stereo-center expansion /scratch/stefan/7901152/working /scratch/stefan/7901152 Bulk generating 3D conformations all protomers in /scratch/stefan/7901152/working/3D mkdir: created directory `/scratch/stefan/7901152/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7901152/working/protonate/xaaaaax_worked-protomers-expanded.ism /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' 92 3D conformations generated for 86 compounds Building REAL300025573507 mkdir: created directory `/scratch/stefan/7901152/working/building' mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573507' /scratch/stefan/7901152/working/building/REAL300025573507 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573507 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573507/0 /scratch/stefan/7901152/working/building/REAL300025573507 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/1 `/scratch/stefan/7901152/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1) `REAL300025573507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573507 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 7, 7, 7, 23, 23, 7, 23, 23, 1, 1, 4, 16, 16, 1, 1, 7, 23, 23, 11, 23, 23, 1, 1] 169 rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 23, 24, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573507 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 44, 73, 73, 45, 73, 158, 157, 158, 169, 169, 158, 169, 165, 73, 73, 44, 8, 8, 73, 73, 158, 169, 169, 168, 169, 169, 73, 73] 169 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 662 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573507 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(C(=O)NC2=CC=CC=C2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 6, 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 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [41, 23, 41, 41, 80, 167, 167, 167, 167, 167, 13, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 23, 23, 41, 80, 80, 23, 23, 5, 1, 1, 1, 1, 1, 23, 23] 167 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, 36, 37]) total number of confs: 435 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573507 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573507 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 mkdir: created directory `/scratch/stefan/7901152/finished' Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573507/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573507 Building REAL300025573508 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573508' /scratch/stefan/7901152/working/building/REAL300025573508 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573508 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573508/0 /scratch/stefan/7901152/working/building/REAL300025573508 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/2 `/scratch/stefan/7901152/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1=CC=C(CCCC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573508 none CC(C)CC1=CC=C(CCCC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 200, 201, 200, 200, 200, 200, 106, 79, 67, 17, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 200, 200, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 106, 106, 99, 99, 67, 67, 16, 8, 8, 200, 200] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573508 none CC(C)CC1=CC=C(CCCC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 3, 1, 1, 1, 1, 1, 1, 2, 6, 10, 47, 47, 47, 73, 199, 199, 199, 199, 199, 1, 1, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 2, 2, 6, 6, 10, 10, 47, 73, 73, 1, 1] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 43, 44, 21, 22] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573508 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573508 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573508/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573508 Building REAL300025573509 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573509' /scratch/stefan/7901152/working/building/REAL300025573509 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573509 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573509/0 /scratch/stefan/7901152/working/building/REAL300025573509 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/3 `/scratch/stefan/7901152/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC(I)=CC([N+](=O)[O-])=C1) `REAL300025573509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573509 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(I)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 18, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 1, 1, 1] 67 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22]) 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: REAL300025573509 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(I)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 18, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 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, 8, 1, 1, 1, 1, 1, 1, 1, 29, 67, 67, 67, 67, 67, 67, 67, 67, 67, 28, 8, 8, 67, 67, 67] 67 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573509 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573509 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573509/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573509 Building REAL300025573510 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573510' /scratch/stefan/7901152/working/building/REAL300025573510 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573510 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573510/0 /scratch/stefan/7901152/working/building/REAL300025573510 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/4 `/scratch/stefan/7901152/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=CC=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025573510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573510 none CCS(=O)(=O)C1=CC=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 152, 97, 152, 152, 97, 40, 97, 97, 40, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 97, 201, 201, 201, 201, 201, 62, 97, 97, 40, 8, 8, 97] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 969 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573510 none CCS(=O)(=O)C1=CC=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 97, 97, 97, 97, 97, 1, 17, 17, 17, 16, 16, 1, 1, 1, 5, 22, 22, 1] 201 rigid atoms, others: [32, 2, 5, 6, 7, 8, 9, 10, 20, 26, 27, 28] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573510 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573510 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573510/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573510 Building REAL300025573511 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573511' /scratch/stefan/7901152/working/building/REAL300025573511 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573511 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573511/0 /scratch/stefan/7901152/working/building/REAL300025573511 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/5 `/scratch/stefan/7901152/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1NCC1=CC=CC=C1) `REAL300025573511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573511 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1NCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 25, 107, 107, 107, 107, 107, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 4, 19, 25, 25, 21, 25, 25, 11, 25, 25, 1, 1, 1, 4, 19, 19, 25, 25, 25, 25, 25] 201 rigid atoms, others: [32, 1, 10, 11, 12, 13, 16, 17, 18, 19, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 289 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573511 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1NCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 26, 107, 107, 107, 107, 107, 107, 107, 107, 107, 155, 201, 201, 201, 201, 201, 201, 26, 8, 8, 107, 107, 107, 155, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 616 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573511 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1NCC1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 75, 75, 103, 201, 201, 201, 201, 201, 25, 25, 19, 25, 25, 25, 25, 25, 15, 3, 1, 1, 1, 1, 1, 1, 1, 75, 103, 103, 25, 25, 25, 15, 3, 3, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 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]) total number of confs: 517 number of broken/clashed sets: 36 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573511 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573511 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573511/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573511 Building REAL300025573512 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573512' /scratch/stefan/7901152/working/building/REAL300025573512 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573512 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573512/0 /scratch/stefan/7901152/working/building/REAL300025573512 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/6 `/scratch/stefan/7901152/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCC1=CC=CC=C1Cl) `REAL300025573512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573512 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 26, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 4, 14, 31, 31, 16, 31, 31, 31, 10, 26, 26, 1, 1, 1, 1, 4, 14, 14, 31, 31, 31, 31] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 308 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573512 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 23, 95, 95, 60, 95, 95, 95, 122, 149, 201, 201, 167, 201, 201, 201, 22, 8, 8, 95, 95, 94, 95, 122, 149, 149, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 814 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573512 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCC1=CC=CC=C1Cl NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 16, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 31, 80, 80, 116, 201, 201, 201, 201, 201, 31, 31, 21, 31, 31, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 80, 116, 116, 31, 31, 31, 31, 19, 6, 6, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 571 number of broken/clashed sets: 32 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573512 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573512 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573512/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573512 Building REAL300025573513 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573513' /scratch/stefan/7901152/working/building/REAL300025573513 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573513 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573513/0 /scratch/stefan/7901152/working/building/REAL300025573513 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/7 `/scratch/stefan/7901152/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(CCCC(=O)NCC2=NC(=O)O[N-]2)C(OC)=C1) `REAL300025573513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573513 none COC1=CC=C(CCCC(=O)NCC2=NC(=O)O[N-]2)C(OC)=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.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 1, 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, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 172, 172, 172, 117, 94, 81, 23, 22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 172, 172, 201, 172, 201, 201, 201, 172, 172, 116, 116, 115, 115, 81, 81, 23, 8, 8, 201, 201, 201, 172] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 835 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573513 none COC1=CC=C(CCCC(=O)NCC2=NC(=O)O[N-]2)C(OC)=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.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 12, 5, 1, 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, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 7, 13, 47, 47, 47, 66, 172, 172, 172, 172, 172, 1, 1, 4, 1, 3, 3, 3, 1, 1, 5, 5, 7, 7, 13, 13, 47, 66, 66, 4, 4, 4, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 19, 20, 22, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 389 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573513 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573513 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573513/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573513 Building REAL300025573514 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573514' /scratch/stefan/7901152/working/building/REAL300025573514 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573514 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573514/0 /scratch/stefan/7901152/working/building/REAL300025573514 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/8 `/scratch/stefan/7901152/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(C(F)(F)F)=C1) `REAL300025573514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573514 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 27, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 1, 1, 1] 67 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23]) total number of confs: 149 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573514 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Br)=CC(C(F)(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 17, 1, 1, 5, 15, 15, 15, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 31, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 30, 8, 8, 67, 67, 67] 67 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573514 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573514 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573514/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573514 Building REAL300025573515 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573515' /scratch/stefan/7901152/working/building/REAL300025573515 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573515 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573515/0 /scratch/stefan/7901152/working/building/REAL300025573515 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/9 `/scratch/stefan/7901152/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C2C(=C1)OCC2CC(=O)NCC1=NC(=O)O[N-]1) `REAL300025573515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573515 none COC1=CC=C2C(=C1)OCC2CC(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 196, 196, 196, 196, 196, 196, 196, 196, 147, 41, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 196, 196, 196, 196, 196, 147, 147, 40, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 720 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573515 none COC1=CC=C2C(=C1)OCC2CC(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 28, 28, 28, 72, 196, 196, 196, 196, 196, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 28, 72, 72] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 25, 26, 27, 28, 29, 30] set([0, 32, 34, 35, 33, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31]) total number of confs: 441 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573515 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573515 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573515/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573515 Building REAL300025573516 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573516' /scratch/stefan/7901152/working/building/REAL300025573516 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573516 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573516/0 /scratch/stefan/7901152/working/building/REAL300025573516 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/10 `/scratch/stefan/7901152/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)N1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1C1CC1) `REAL300025573516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573516 none CCC(C)N1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [168, 167, 129, 167, 129, 129, 129, 40, 39, 39, 8, 1, 1, 1, 1, 1, 1, 1, 129, 129, 139, 139, 168, 168, 168, 168, 168, 167, 167, 167, 167, 129, 39, 8, 8, 139, 139, 139, 139, 139] 170 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 483 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573516 none CCC(C)N1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 5, 1, 5, 1, 1, 1, 1, 1, 12, 12, 12, 46, 129, 129, 129, 129, 129, 1, 1, 4, 4, 11, 11, 11, 11, 11, 5, 6, 6, 6, 1, 12, 46, 46, 4, 4, 4, 4, 4] 170 rigid atoms, others: [2, 4, 5, 6, 7, 8, 18, 19, 31] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573516 none CCC(C)N1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [12, 8, 4, 8, 4, 4, 4, 4, 4, 20, 20, 20, 57, 139, 139, 139, 139, 139, 1, 1, 1, 1, 13, 13, 13, 13, 13, 8, 8, 8, 8, 4, 20, 57, 57, 1, 1, 1, 1, 1] 170 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]) total number of confs: 365 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573516 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573516 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573516/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573516 Building REAL300025573517 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573517' /scratch/stefan/7901152/working/building/REAL300025573517 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573517 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573517/0 /scratch/stefan/7901152/working/building/REAL300025573517 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/11 `/scratch/stefan/7901152/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCSC1=CC=C([N+](=O)[O-])C=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573517 none COCCSC1=CC=C([N+](=O)[O-])C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 175, 127, 74, 74, 74, 42, 74, 74, 74, 74, 74, 29, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 175, 175, 74, 74, 74, 28, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 764 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573517 none COCCSC1=CC=C([N+](=O)[O-])C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 14, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 39, 25, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 74, 74, 74, 74, 74, 53, 53, 53, 39, 39, 25, 25, 1, 1, 1, 7, 17, 17] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573517 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573517 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573517/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573517 Building REAL300025573518 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573518' /scratch/stefan/7901152/working/building/REAL300025573518 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573518 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573518/0 /scratch/stefan/7901152/working/building/REAL300025573518 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/12 `/scratch/stefan/7901152/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(Br)C=C2)C=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573518 none CC1=NN(C2=CC=C(Br)C=C2)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 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, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 17, 17, 28, 55, 55, 55, 55, 55, 4, 4, 4, 1, 1, 1, 1, 3, 17, 28, 28] 55 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28, 29] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 139 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: REAL300025573518 none CC1=NN(C2=CC=C(Br)C=C2)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 1, 3, 3, 1, 1, 1, 12, 12, 12, 25, 54, 54, 54, 55, 55, 2, 2, 2, 3, 3, 3, 3, 1, 12, 25, 25] 55 rigid atoms, others: [0, 1, 2, 3, 4, 11, 12, 13, 30] set([5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 144 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: REAL300025573518 none CC1=NN(C2=CC=C(Br)C=C2)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 55 conformations in input total number of sets (complete confs): 55 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 38, 37, 37, 8, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 38, 8, 8] 55 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 128 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573518 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573518 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573518/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573518 Building REAL300025573519 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573519' /scratch/stefan/7901152/working/building/REAL300025573519 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573519 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573519/0 /scratch/stefan/7901152/working/building/REAL300025573519 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/13 `/scratch/stefan/7901152/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CSC(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=N2)=N1) `REAL300025573519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573519 none CCC1=CSC(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 4, 4, 4, 4, 1, 1, 1, 1, 1, 5, 5, 5, 27, 111, 111, 111, 111, 111, 1, 1, 4, 19, 19, 19, 19, 19, 4, 1, 5, 27, 27, 1] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 19, 20, 28] set([0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) 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: REAL300025573519 none CCC1=CSC(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 41, 140, 140, 140, 140, 140, 4, 4, 1, 9, 9, 9, 9, 9, 1, 4, 12, 41, 41, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 21, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573519 none CCC1=CSC(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=N2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 14, 1, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 140, 140, 140, 140, 111, 111, 111, 45, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 111, 111, 140, 201, 201, 201, 201, 201, 140, 111, 44, 8, 8, 111] 201 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573519 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573519 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573519/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573519 Building REAL300025573520 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573520' /scratch/stefan/7901152/working/building/REAL300025573520 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573520 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573520/0 /scratch/stefan/7901152/working/building/REAL300025573520 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/14 `/scratch/stefan/7901152/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CNC2=CC=CC([N+](=O)[O-])=C12) `REAL300025573520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573520 none O=C(NCC1=NC(=O)O[N-]1)C1=CNC2=CC=CC([N+](=O)[O-])=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 3, 13, 13, 1, 1, 1, 1, 1] 27 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 22, 23, 24]) 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: REAL300025573520 none O=C(NCC1=NC(=O)O[N-]1)C1=CNC2=CC=CC([N+](=O)[O-])=C12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 1, 1, 1, 1, 1, 8, 11, 11, 1, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 21, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 8, 8, 27, 27, 27, 27, 27] 27 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573520 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573520 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573520/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573520 Building REAL300025573521 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573521' /scratch/stefan/7901152/working/building/REAL300025573521 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573521 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573521/0 /scratch/stefan/7901152/working/building/REAL300025573521 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/15 `/scratch/stefan/7901152/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCSC1=CC=CC=C1Br)NCC1=NC(=O)O[N-]1) `REAL300025573521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573521 none O=C(CCSC1=CC=CC=C1Br)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 11, 75, 75, 151, 201, 201, 182, 201, 201, 200, 8, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 201, 201, 182, 200, 10, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 511 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573521 none O=C(CCSC1=CC=CC=C1Br)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 14, 1, 1, 1, 1, 1, 1, 17, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 108, 201, 201, 201, 201, 201, 20, 20, 20, 20, 1, 1, 1, 1, 106, 108, 108] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30]) total number of confs: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573521 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573521 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573521/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573521 Building REAL300025573522 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573522' /scratch/stefan/7901152/working/building/REAL300025573522 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573522 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573522/0 /scratch/stefan/7901152/working/building/REAL300025573522 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/16 `/scratch/stefan/7901152/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1)NCC1=NC(=O)O[N-]1) `REAL300025573522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573522 none O=C(COC1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 62, 107, 201, 201, 201, 201, 201, 201, 107, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 62, 62, 201, 107, 201, 11, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573522 none O=C(COC1=CC(C(F)(F)F)=CC(C(F)(F)F)=C1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 18, 6, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 93, 93, 96, 201, 201, 201, 201, 201, 18, 18, 1, 1, 1, 93, 96, 96] 201 rigid atoms, others: [3, 4, 5, 6, 7, 11, 12, 13, 17, 28, 29, 30] set([0, 1, 2, 8, 9, 10, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573522 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573522 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573522/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573522 Building REAL300025573523 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573523' /scratch/stefan/7901152/working/building/REAL300025573523 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573523 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573523/0 /scratch/stefan/7901152/working/building/REAL300025573523 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/17 `/scratch/stefan/7901152/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NC1(C)CCCCC1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573523 none CC(C)(C)OC(=O)NC1(C)CCCCC1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 89, 62, 89, 62, 62, 62, 62, 62, 62, 62, 36, 35, 35, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 35, 8, 8] 127 rigid atoms, others: [18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573523 none CC(C)(C)OC(=O)NC1(C)CCCCC1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 11, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 62, 62, 62, 62, 62, 12, 12, 12, 11, 11, 11, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 20, 20] 127 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 47, 48, 49]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573523 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573523 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573523/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573523 Building REAL300025573524 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573524' /scratch/stefan/7901152/working/building/REAL300025573524 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573524 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573524/0 /scratch/stefan/7901152/working/building/REAL300025573524 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/18 `/scratch/stefan/7901152/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(=O)NC1=CC=C2NC(=O)NC2=N1)NCC1=NC(=O)O[N-]1) `REAL300025573524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573524 none O=C(CCC(=O)NC1=CC=C2NC(=O)NC2=N1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 1, 8, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 3, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 30, 31, 116, 141, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 116, 116, 141, 141, 174, 201, 201, 201, 201, 30, 8, 8] 201 rigid atoms, others: [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: 735 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573524 none O=C(CCC(=O)NC1=CC=C2NC(=O)NC2=N1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 1, 8, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 7, 6, 4, 7, 3, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 23, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 105, 201, 201, 201, 201, 201, 23, 23, 15, 15, 3, 1, 1, 1, 1, 69, 105, 105] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573524 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573524 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573524/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573524 Building REAL300025573525 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573525' /scratch/stefan/7901152/working/building/REAL300025573525 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573525 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573525/0 /scratch/stefan/7901152/working/building/REAL300025573525 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/19 `/scratch/stefan/7901152/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=NC(C(=O)NCC3=NC(=O)O[N-]3)=CS2)N1C) `REAL300025573525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573525 none CC1=CC=C(C2=NC(C(=O)NCC3=NC(=O)O[N-]3)=CS2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 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: [10, 10, 10, 10, 1, 1, 1, 1, 1, 12, 12, 12, 33, 89, 89, 89, 89, 89, 1, 1, 10, 10, 10, 10, 10, 10, 10, 12, 32, 32, 1, 10, 10, 10] 139 rigid atoms, others: [4, 5, 6, 7, 8, 18, 19, 30] set([0, 1, 2, 3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) 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: REAL300025573525 none CC1=CC=C(C2=NC(C(=O)NCC3=NC(=O)O[N-]3)=CS2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 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, 1, 1, 10, 10, 10, 47, 47, 47, 89, 139, 139, 139, 139, 139, 10, 10, 1, 1, 2, 2, 2, 1, 1, 47, 89, 89, 10, 2, 2, 2] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 393 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573525 none CC1=CC=C(C2=NC(C(=O)NCC3=NC(=O)O[N-]3)=CS2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'S.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 14, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 89, 89, 89, 44, 43, 43, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 139, 139, 139, 139, 139, 139, 139, 43, 8, 8, 89, 139, 139, 139] 139 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 275 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573525 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573525 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573525/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573525 Building REAL300025573526 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573526' /scratch/stefan/7901152/working/building/REAL300025573526 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573526 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573526/0 /scratch/stefan/7901152/working/building/REAL300025573526 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/20 `/scratch/stefan/7901152/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC2=CC(C(=O)NCC3=NC(=O)O[N-]3)=CC=C21) `REAL300025573526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573526 none CN1C(=O)CCC2=CC(C(=O)NCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 19, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 57, 57, 19, 57, 57, 57, 57, 57, 57, 57, 57, 18, 8, 8, 57, 57] 57 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: 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: REAL300025573526 none CN1C(=O)CCC2=CC(C(=O)NCC3=NC(=O)O[N-]3)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20, 20, 1, 1] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34] set([32, 10, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573526 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573526 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573526/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573526 Building REAL300025573527 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573527' /scratch/stefan/7901152/working/building/REAL300025573527 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573527 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573527/0 /scratch/stefan/7901152/working/building/REAL300025573527 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/21 `/scratch/stefan/7901152/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1CCOC1CCCCO1) `REAL300025573527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573527 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1CCOC1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 12, 5, 5, 5, 5, 5, 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, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 21, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 138, 146, 184, 201, 201, 201, 201, 201, 54, 54, 54, 21, 8, 8, 54, 138, 138, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573527 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1CCOC1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 12, 5, 5, 5, 5, 5, 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, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 16, 54, 54, 54, 54, 54, 1, 1, 1, 1, 6, 8, 28, 45, 45, 45, 45, 45, 2, 2, 2, 8, 16, 16, 1, 6, 6, 8, 8, 45, 45, 45, 45, 45, 45, 45, 45, 45] 201 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 16, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573527 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1CCOC1CCCCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 5, 5, 12, 5, 5, 5, 5, 5, 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, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 105, 105, 105, 116, 201, 201, 201, 201, 201, 45, 45, 15, 13, 7, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 105, 116, 116, 45, 15, 15, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 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]) total number of confs: 458 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573527 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573527 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573527/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573527 Building REAL300025573528 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573528' /scratch/stefan/7901152/working/building/REAL300025573528 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573528 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573528/0 /scratch/stefan/7901152/working/building/REAL300025573528 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/22 `/scratch/stefan/7901152/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OCC(F)F)=C1) `REAL300025573528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573528 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OCC(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 4, 17, 42, 42, 1, 5, 13, 13, 1, 1, 17, 17, 42, 1] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 20, 24, 25, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28]) total number of confs: 291 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573528 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OCC(F)F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 25, 76, 76, 76, 76, 76, 127, 199, 201, 201, 76, 24, 8, 8, 76, 76, 199, 199, 201, 76] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 614 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573528 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573528 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573528/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573528 Building REAL300025573529 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573529' /scratch/stefan/7901152/working/building/REAL300025573529 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573529 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573529/0 /scratch/stefan/7901152/working/building/REAL300025573529 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/23 `/scratch/stefan/7901152/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC(Br)=CC=C1F)NCC1=NC(=O)O[N-]1) `REAL300025573529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573529 none O=C(CCC1=CC(Br)=CC=C1F)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 122, 154, 201, 201, 201, 189, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 122, 122, 154, 154, 201, 189, 201, 40, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573529 none O=C(CCC1=CC(Br)=CC=C1F)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 17, 1, 1, 1, 15, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 99, 201, 201, 201, 201, 201, 15, 15, 7, 7, 1, 1, 1, 55, 99, 99] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 10, 11, 24, 25, 26] set([0, 1, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573529 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573529 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573529/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573529 Building REAL300025573530 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573530' /scratch/stefan/7901152/working/building/REAL300025573530 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573530 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573530/0 /scratch/stefan/7901152/working/building/REAL300025573530 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/24 `/scratch/stefan/7901152/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1=CC=C(Cl)C=C1Cl) `REAL300025573530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573530 none CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 56, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1, 135, 135, 135, 166, 166, 166, 166, 166, 166, 166, 135, 135, 135, 134, 55, 8, 8, 166, 166, 166] 166 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 312 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573530 none CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 40, 134, 134, 135, 134, 134, 1, 1, 1, 7, 7, 2, 6, 7, 7, 7, 2, 2, 2, 1, 12, 40, 40, 7, 7, 7] 166 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573530 none CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1=CC=C(Cl)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 51, 51, 51, 89, 166, 166, 166, 166, 166, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 51, 89, 89, 1, 1, 1] 166 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 409 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573530 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573530 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573530/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573530 Building REAL300025573531 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573531' /scratch/stefan/7901152/working/building/REAL300025573531 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573531 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573531/0 /scratch/stefan/7901152/working/building/REAL300025573531 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/25 `/scratch/stefan/7901152/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1CCCCC1) `REAL300025573531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573531 none CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [89, 89, 89, 45, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 99, 99, 99, 99, 99, 89, 89, 89, 89, 44, 8, 8, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99] 99 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 222 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: REAL300025573531 none CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 12, 12, 12, 31, 88, 88, 88, 88, 88, 1, 1, 1, 5, 5, 5, 5, 5, 2, 2, 2, 1, 12, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 99 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 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: 202 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: REAL300025573531 none CC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=NN1C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', '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'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 5, 5, 27, 27, 28, 55, 99, 99, 99, 99, 99, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 5, 27, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 251 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573531 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573531 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573531/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573531 Building REAL300025573532 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573532' /scratch/stefan/7901152/working/building/REAL300025573532 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573532 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573532/0 /scratch/stefan/7901152/working/building/REAL300025573532 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/26 `/scratch/stefan/7901152/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CN=C1OCC(F)F) `REAL300025573532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573532 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CN=C1OCC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 22, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 5, 24, 38, 38, 13, 22, 22, 1, 1, 1, 24, 24, 38] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573532 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CN=C1OCC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 1, 12, 5, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 16, 77, 77, 77, 77, 77, 77, 142, 201, 201, 201, 15, 8, 8, 77, 77, 77, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573532 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573532 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573532/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573532 Building REAL300025573533 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573533' /scratch/stefan/7901152/working/building/REAL300025573533 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573533 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573533/0 /scratch/stefan/7901152/working/building/REAL300025573533 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/27 `/scratch/stefan/7901152/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=NC(=O)O[N-]2)NC(C2=CC(C)=CC=C2)=N1) `REAL300025573533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573533 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)NC(C2=CC(C)=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 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] 0 hydrogens 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, 35, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 201, 201, 201, 110, 201, 201, 110, 110, 110, 110, 34, 8, 8, 110, 201, 201, 201, 201, 178, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 695 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573533 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)NC(C2=CC(C)=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 29, 109, 109, 109, 109, 109, 1, 1, 1, 13, 13, 13, 1, 13, 13, 1, 2, 2, 2, 9, 29, 29, 1, 13, 13, 13, 13, 1, 13, 13] 201 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 22, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573533 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)NC(C2=CC(C)=CC=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 5, 1, 1, 1, 8, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 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] 0 hydrogens 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, 76, 76, 76, 128, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 76, 128, 128, 13, 1, 2, 2, 2, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 563 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573533 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573533 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573533/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573533 Building REAL300025573534 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573534' /scratch/stefan/7901152/working/building/REAL300025573534 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573534 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573534/0 /scratch/stefan/7901152/working/building/REAL300025573534 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/28 `/scratch/stefan/7901152/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCCC1=CCCCC1) `REAL300025573534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573534 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCCC1=CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 25, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 4, 10, 20, 31, 31, 31, 31, 31, 12, 25, 25, 1, 1, 1, 1, 4, 10, 10, 20, 20, 31, 31, 31, 31, 31, 31, 31, 31, 31] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 277 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: REAL300025573534 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCCC1=CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 27, 103, 103, 64, 103, 103, 103, 138, 162, 196, 201, 201, 201, 201, 201, 26, 8, 8, 103, 103, 103, 103, 138, 162, 162, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 806 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573534 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC=C1NCCC1=CCCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 31, 94, 94, 117, 201, 201, 201, 201, 201, 31, 31, 19, 31, 31, 19, 9, 6, 1, 1, 1, 1, 1, 1, 1, 94, 117, 117, 31, 31, 31, 31, 19, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [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, 35, 36]) total number of confs: 576 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573534 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573534 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573534/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573534 Building REAL300025573535 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573535' /scratch/stefan/7901152/working/building/REAL300025573535 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573535 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573535/0 /scratch/stefan/7901152/working/building/REAL300025573535 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/29 `/scratch/stefan/7901152/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)F)N=C1) `REAL300025573535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573535 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 13, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 4, 22, 50, 50, 1, 1, 5, 13, 13, 1, 1, 22, 22, 50, 1] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 19, 20, 24, 25, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28]) 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: REAL300025573535 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OCC(F)F)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 8, 1, 1, 1, 1, 1, 1, 1, 23, 69, 69, 69, 69, 115, 199, 201, 201, 69, 69, 22, 8, 8, 69, 69, 199, 199, 201, 69] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 628 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573535 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573535 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573535/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573535 Building REAL300025573536 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573536' /scratch/stefan/7901152/working/building/REAL300025573536 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025573536 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573536/0 /scratch/stefan/7901152/working/building/REAL300025573536 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/30 `/scratch/stefan/7901152/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=NC=C1) `REAL300025573536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573536 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 54, 53, 53, 8, 1, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 179, 179, 179, 179, 179, 173, 173, 173, 53, 8, 8, 173, 179, 179, 179, 179] 179 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 313 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: REAL300025573536 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 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 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, 11, 11, 11, 52, 173, 173, 173, 173, 173, 1, 1, 1, 1, 6, 6, 1, 6, 6, 2, 2, 2, 11, 52, 52, 1, 6, 6, 6, 6] 179 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 16, 28] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 359 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573536 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=NC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 37, 37, 37, 106, 179, 179, 179, 179, 179, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 37, 106, 106, 6, 1, 1, 1, 1] 179 rigid atoms, others: [32, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 479 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573536 /scratch/stefan/7901152/working /scratch/stefan/7901152 mkdir: created directory `1' /scratch/stefan/7901152/working/building/REAL300025573536/1 /scratch/stefan/7901152/working/building/REAL300025573536 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/31 `/scratch/stefan/7901152/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=[NH+]C=C1) `REAL300025573536.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025573536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573536 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 53, 52, 52, 8, 1, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 179, 179, 175, 179, 179, 179, 175, 175, 175, 53, 8, 8, 175, 179, 179, 179, 179] 179 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 332 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: REAL300025573536 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 11, 11, 52, 175, 175, 175, 175, 175, 1, 1, 1, 1, 6, 6, 1, 1, 6, 6, 2, 2, 2, 11, 52, 52, 1, 6, 6, 6, 6] 179 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 16, 29] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 358 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: REAL300025573536 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=[NH+]C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 8, 6, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 41, 41, 41, 112, 179, 179, 179, 179, 179, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 41, 112, 112, 6, 1, 1, 1, 1] 179 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 484 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573536 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573536 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 1: /scratch/stefan/7901152/working/building/REAL300025573536/1.* 0: /scratch/stefan/7901152/working/building/REAL300025573536/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573536 Building REAL300025573537 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573537' /scratch/stefan/7901152/working/building/REAL300025573537 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573537 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573537/0 /scratch/stefan/7901152/working/building/REAL300025573537 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/32 `/scratch/stefan/7901152/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2C=C1OC(F)F) `REAL300025573537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573537 none O=C(NCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2C=C1OC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 13, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 17, 17, 7, 13, 13, 1, 1, 1, 1, 1, 1, 17] 35 rigid atoms, others: [32, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 33, 2, 3, 4, 5, 6, 7, 8, 9, 21, 22, 23, 24, 25, 26]) total number of confs: 132 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573537 none O=C(NCC1=NC(=O)O[N-]1)C1=CC2=CC=CC=C2C=C1OC(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 35, 35, 27, 8, 8, 31, 31, 31, 31, 31, 31, 35] 35 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573537 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573537 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573537/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573537 Building REAL300025573538 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573538' /scratch/stefan/7901152/working/building/REAL300025573538 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573538 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573538/0 /scratch/stefan/7901152/working/building/REAL300025573538 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/33 `/scratch/stefan/7901152/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(F)(F)F)C(C)=C1CC(=O)NCC1=NC(=O)O[N-]1) `REAL300025573538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573538 none CC1=NN(CC(F)(F)F)C(C)=C1CC(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 5, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 201, 201, 201, 201, 120, 120, 76, 12, 11, 11, 8, 1, 1, 1, 1, 1, 1, 1, 120, 120, 120, 201, 201, 120, 120, 120, 76, 76, 11, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573538 none CC1=NN(CC(F)(F)F)C(C)=C1CC(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 15, 15, 15, 1, 5, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations 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, 5, 5, 5, 6, 1, 1, 1, 1, 4, 26, 26, 27, 35, 119, 120, 119, 120, 120, 2, 2, 2, 5, 5, 2, 2, 2, 4, 4, 26, 35, 35] 201 rigid atoms, others: [0, 1, 2, 3, 4, 9, 10, 11, 12] set([5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573538 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573538 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573538/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573538 Building REAL300025573539 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573539' /scratch/stefan/7901152/working/building/REAL300025573539 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573539 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573539/0 /scratch/stefan/7901152/working/building/REAL300025573539 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/34 `/scratch/stefan/7901152/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(CC(=O)NCC2=NC(=O)O[N-]2)CCCCC1) `REAL300025573539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573539 none CC(C)(C)OC(=O)NCC1(CC(=O)NCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 201, 105, 92, 37, 17, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 167, 105, 105, 37, 37, 17, 8, 8, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 728 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: REAL300025573539 none CC(C)(C)OC(=O)NCC1(CC(=O)NCC2=NC(=O)O[N-]2)CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 27, 15, 27, 5, 1, 1, 1, 10, 19, 19, 19, 31, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 5, 5, 10, 10, 19, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [8, 9, 10, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 295 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573539 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573539 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573539/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573539 Building REAL300025573540 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573540' /scratch/stefan/7901152/working/building/REAL300025573540 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573540 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573540/0 /scratch/stefan/7901152/working/building/REAL300025573540 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/35 `/scratch/stefan/7901152/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCCC1(C)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573540 none CC(C)(C)OC(=O)N1CCCCC1(C)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 144, 86, 144, 86, 86, 86, 86, 86, 50, 86, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 163, 163, 163, 163, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 50, 8, 8] 163 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 478 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573540 none CC(C)(C)OC(=O)N1CCCCC1(C)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [20, 18, 20, 20, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 86, 86, 86, 86, 86, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 20, 20] 163 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573540 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573540 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573540/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573540 Building REAL300025573541 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573541' /scratch/stefan/7901152/working/building/REAL300025573541 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573541 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573541/0 /scratch/stefan/7901152/working/building/REAL300025573541 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/36 `/scratch/stefan/7901152/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(=O)(=O)C1=CC=CC(CC(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025573541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573541 none CCS(=O)(=O)C1=CC=CC(CC(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 161, 153, 161, 161, 153, 127, 153, 153, 89, 34, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 136, 201, 201, 201, 201, 201, 127, 153, 153, 89, 89, 34, 8, 8, 153] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 860 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573541 none CCS(=O)(=O)C1=CC=CC(CC(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 11, 11, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 43, 153, 153, 153, 153, 153, 1, 10, 10, 10, 9, 9, 1, 1, 1, 6, 6, 15, 43, 43, 1] 201 rigid atoms, others: [2, 35, 5, 6, 7, 8, 9, 10, 21, 27, 28, 29] set([0, 1, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573541 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573541 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573541/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573541 Building REAL300025573542 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573542' /scratch/stefan/7901152/working/building/REAL300025573542 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573542 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573542/0 /scratch/stefan/7901152/working/building/REAL300025573542 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/37 `/scratch/stefan/7901152/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1=CC(Cl)=CC=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573542 none CCSC1=CC(Cl)=CC=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 97, 97, 97, 56, 97, 97, 97, 32, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 97, 97, 97, 31, 8, 8] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 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: REAL300025573542 none CCSC1=CC(Cl)=CC=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 28, 97, 97, 97, 97, 97, 29, 29, 29, 29, 29, 1, 1, 1, 8, 28, 28] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573542 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573542 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573542/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573542 Building REAL300025573543 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573543' /scratch/stefan/7901152/working/building/REAL300025573543 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573543 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573543/0 /scratch/stefan/7901152/working/building/REAL300025573543 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/38 `/scratch/stefan/7901152/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(=O)C1=CC=C2NC(=O)CCC2=C1)NCC1=NC(=O)O[N-]1) `REAL300025573543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573543 none O=C(CCC(=O)C1=CC=C2NC(=O)CCC2=C1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 24, 88, 107, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 88, 88, 107, 107, 200, 200, 201, 201, 201, 201, 201, 201, 24, 8, 8] 201 rigid atoms, others: [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]) total number of confs: 660 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573543 none O=C(CCC(=O)C1=CC=C2NC(=O)CCC2=C1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 31, 26, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 92, 115, 200, 200, 200, 200, 200, 31, 31, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 92, 115, 115] 201 rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 36, 29, 30, 31] set([0, 1, 2, 3, 5, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 546 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573543 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573543 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573543/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573543 Building REAL300025573544 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573544' /scratch/stefan/7901152/working/building/REAL300025573544 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573544 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573544/0 /scratch/stefan/7901152/working/building/REAL300025573544 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/39 `/scratch/stefan/7901152/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(Br)C(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025573544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573544 none CC1=CC(C)=C(Br)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 17, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 33, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 32, 8, 8, 61] 61 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573544 none CC1=CC(C)=C(Br)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'Br', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 17, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 61, 61, 61, 61, 61, 1, 2, 2, 2, 1, 2, 2, 2, 7, 27, 27, 1] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 22, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 23, 24, 25, 26, 27, 28]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573544 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573544 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573544/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573544 Building REAL300025573545 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573545' /scratch/stefan/7901152/working/building/REAL300025573545 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573545 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573545/0 /scratch/stefan/7901152/working/building/REAL300025573545 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/40 `/scratch/stefan/7901152/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1=C(C(=O)NCC2=NC(=O)O[N-]2)C=NN1C1=CC=CC=C1) `REAL300025573545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573545 none COCC1=C(C(=O)NCC2=NC(=O)O[N-]2)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.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 196, 131, 132, 43, 42, 42, 8, 1, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 170, 170, 162, 170, 170, 201, 201, 201, 196, 196, 42, 8, 8, 132, 170, 170, 162, 170, 170] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 654 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: REAL300025573545 none COCC1=C(C(=O)NCC2=NC(=O)O[N-]2)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.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 6, 1, 1, 1, 1, 9, 9, 9, 35, 131, 131, 131, 131, 131, 1, 1, 1, 1, 5, 5, 3, 5, 5, 21, 21, 21, 6, 6, 9, 35, 35, 1, 5, 5, 3, 5, 5] 201 rigid atoms, others: [32, 2, 3, 4, 5, 15, 16, 17, 18] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37]) total number of confs: 302 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: REAL300025573545 none COCC1=C(C(=O)NCC2=NC(=O)O[N-]2)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.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 15, 5, 5, 5, 5, 26, 26, 26, 69, 170, 170, 170, 170, 170, 5, 5, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 15, 15, 26, 69, 69, 5, 1, 1, 1, 1, 1] 201 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: 472 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573545 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573545 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573545/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573545 Building REAL300025573546 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573546' /scratch/stefan/7901152/working/building/REAL300025573546 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573546 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573546/0 /scratch/stefan/7901152/working/building/REAL300025573546 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/41 `/scratch/stefan/7901152/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1CC1C1=CC(F)=C(F)C(F)=C1) `REAL300025573546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573546 none O=C(NCC1=NC(=O)O[N-]1)C1CC1C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 66, 150, 150, 150, 150, 150, 1, 1, 1, 1, 7, 7, 7, 2, 3, 7, 7, 7, 13, 66, 66, 1, 1, 1, 1, 7, 7] 195 rigid atoms, others: [1, 10, 11, 12, 13, 25, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30]) total number of confs: 363 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: REAL300025573546 none O=C(NCC1=NC(=O)O[N-]1)C1CC1C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [52, 52, 8, 1, 1, 1, 1, 1, 1, 1, 53, 150, 150, 150, 195, 195, 195, 194, 195, 195, 195, 195, 52, 8, 8, 150, 150, 150, 150, 195, 195] 195 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 498 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: REAL300025573546 none O=C(NCC1=NC(=O)O[N-]1)C1CC1C1=CC(F)=C(F)C(F)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 1, 15, 1, 15, 1, 15, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [54, 7, 54, 54, 125, 196, 196, 196, 196, 196, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 125, 125, 7, 7, 7, 7, 1, 1] 196 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 559 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573546 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573546 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573546/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573546 Building REAL300025573547 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573547' /scratch/stefan/7901152/working/building/REAL300025573547 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573547 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573547/0 /scratch/stefan/7901152/working/building/REAL300025573547 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/42 `/scratch/stefan/7901152/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300025573547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573547 none CC(C)(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 44, 44, 44, 100, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 44, 100, 100, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 516 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573547 none CC(C)(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [153, 45, 153, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 153, 153, 153, 153, 45, 8, 8, 201, 201, 201] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573547 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573547 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573547/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573547 Building REAL300025573548 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573548' /scratch/stefan/7901152/working/building/REAL300025573548 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025573548 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573548/0 /scratch/stefan/7901152/working/building/REAL300025573548 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/43 `/scratch/stefan/7901152/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(I)C(O)=C1) `REAL300025573548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573548 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(I)C(O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 23, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 1, 1, 2, 1] 134 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 23]) 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: REAL300025573548 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(I)C(O)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 19, 67, 67, 66, 67, 67, 67, 67, 18, 8, 8, 67, 67, 134, 67] 134 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573548 /scratch/stefan/7901152/working /scratch/stefan/7901152 mkdir: created directory `1' /scratch/stefan/7901152/working/building/REAL300025573548/1 /scratch/stefan/7901152/working/building/REAL300025573548 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/44 `/scratch/stefan/7901152/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(I)C([O-])=C1) `REAL300025573548.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025573548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573548 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(I)C([O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 7, 25, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 7, 25, 25, 1, 1, 1] 49 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573548 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(I)C([O-])=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 18, 1, 12, 1, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 3, 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, 25, 8, 1, 1, 1, 1, 1, 1, 1, 26, 49, 49, 49, 49, 49, 49, 49, 26, 8, 8, 49, 49, 49] 49 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573548 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573548 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 1: /scratch/stefan/7901152/working/building/REAL300025573548/1.* 0: /scratch/stefan/7901152/working/building/REAL300025573548/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573548 Building REAL300025573549 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573549' /scratch/stefan/7901152/working/building/REAL300025573549 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573549 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573549/0 /scratch/stefan/7901152/working/building/REAL300025573549 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/45 `/scratch/stefan/7901152/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC1=CC=C([N+](=O)[O-])C=C1)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573549 none CCC(CC1=CC=C([N+](=O)[O-])C=C1)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [154, 140, 52, 140, 194, 201, 201, 201, 201, 201, 201, 201, 201, 51, 51, 8, 1, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 140, 194, 194, 201, 201, 201, 201, 51, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1065 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: REAL300025573549 none CCC(CC1=CC=C([N+](=O)[O-])C=C1)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 24, 24, 24, 82, 201, 201, 201, 201, 201, 11, 11, 11, 11, 11, 7, 3, 3, 1, 1, 1, 1, 24, 82, 82] 201 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37]) total number of confs: 488 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573549 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573549 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573549/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573549 Building REAL300025573550 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573550' /scratch/stefan/7901152/working/building/REAL300025573550 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573550 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573550/0 /scratch/stefan/7901152/working/building/REAL300025573550 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/46 `/scratch/stefan/7901152/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(F)C=C2F)C=C1) `REAL300025573550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573550 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 34, 96, 96, 96, 97, 97, 1, 1, 1, 1, 8, 8, 2, 8, 8, 8, 8, 1, 1, 12, 34, 34, 8, 8, 8, 1, 1] 123 rigid atoms, others: [1, 10, 11, 12, 13, 21, 22, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28]) 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: REAL300025573550 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 45, 97, 97, 97, 123, 123, 121, 123, 123, 123, 123, 97, 97, 45, 8, 8, 122, 123, 123, 97, 97] 123 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) 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: REAL300025573550 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=C(F)C=C2F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 15, 1, 1, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 8, 41, 41, 67, 123, 123, 123, 123, 123, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 41, 67, 67, 1, 1, 1, 8, 8] 123 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 29, 30]) total number of confs: 314 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573550 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573550 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573550/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573550 Building REAL300025573551 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573551' /scratch/stefan/7901152/working/building/REAL300025573551 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573551 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573551/0 /scratch/stefan/7901152/working/building/REAL300025573551 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/47 `/scratch/stefan/7901152/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC1C(=O)NCCC(=O)NCC1=NC(=O)O[N-]1) `REAL300025573551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573551 none CC(C)(C)OC(=O)N1CCCC1C(=O)NCCC(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 160, 201, 160, 160, 160, 160, 152, 152, 152, 109, 76, 31, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 160, 160, 152, 109, 109, 76, 76, 30, 8, 8] 201 rigid atoms, others: [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, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 758 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573551 none CC(C)(C)OC(=O)N1CCCC1C(=O)NCCC(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 20, 59, 58, 58, 74, 160, 160, 160, 160, 160, 3, 3, 3, 2, 2, 2, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 20, 20, 59, 74, 74] 201 rigid atoms, others: [36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 42, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573551 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573551 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573551/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573551 Building REAL300025573552 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573552' /scratch/stefan/7901152/working/building/REAL300025573552 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573552 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573552/0 /scratch/stefan/7901152/working/building/REAL300025573552 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/48 `/scratch/stefan/7901152/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC(C(=O)NCC3=NC(=O)O[N-]3)=NO2)CC1) `REAL300025573552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573552 none CC(C)(C)OC(=O)N1CCC2(CC(C(=O)NCC3=NC(=O)O[N-]3)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 137, 108, 137, 108, 108, 108, 108, 108, 41, 40, 40, 8, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 108, 108, 108, 108, 108, 41, 8, 8, 108, 108, 108, 108] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 426 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573552 none CC(C)(C)OC(=O)N1CCC2(CC(C(=O)NCC3=NC(=O)O[N-]3)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 30, 107, 107, 107, 107, 107, 1, 1, 1, 1, 11, 11, 11, 10, 10, 10, 11, 11, 11, 1, 1, 1, 1, 1, 1, 12, 30, 30, 1, 1, 1, 1] 201 rigid atoms, others: [5, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573552 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573552 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573552/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573552 Building REAL300025573553 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573553' /scratch/stefan/7901152/working/building/REAL300025573553 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573553 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573553/0 /scratch/stefan/7901152/working/building/REAL300025573553 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/49 `/scratch/stefan/7901152/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)CC(C)(C)CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573553 none COC1=CC=C(C(=O)CC(C)(C)CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 201, 201, 166, 145, 166, 85, 40, 85, 85, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 145, 145, 85, 85, 85, 85, 85, 85, 40, 40, 20, 8, 8, 201, 201] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 935 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573553 none COC1=CC=C(C(=O)CC(C)(C)CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 33, 33, 33, 52, 95, 95, 95, 110, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 15, 15, 33, 33, 33, 33, 33, 33, 52, 52, 95, 110, 110, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 23, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573553 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573553 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573553/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573553 Building REAL300025573554 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573554' /scratch/stefan/7901152/working/building/REAL300025573554 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573554 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573554/0 /scratch/stefan/7901152/working/building/REAL300025573554 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/50 `/scratch/stefan/7901152/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1Br) `REAL300025573554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573554 none CN1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 34, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 33, 8, 8] 61 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23]) 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: REAL300025573554 none CN1N=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1Br NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'Br', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 17, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 61, 61, 61, 61, 61, 1, 1, 2, 2, 2, 1, 6, 25, 25] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 15, 16, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 21, 22, 23]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573554 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573554 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573554/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573554 Building REAL300025573555 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573555' /scratch/stefan/7901152/working/building/REAL300025573555 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025573555 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573555/0 /scratch/stefan/7901152/working/building/REAL300025573555 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/51 `/scratch/stefan/7901152/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC=C([O-])C(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025573555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573555 none CN(C)S(=O)(=O)C1=CC=C([O-])C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 201, 201, 104, 63, 104, 104, 104, 49, 48, 48, 8, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 104, 104, 48, 8, 8, 104] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 833 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573555 none CN(C)S(=O)(=O)C1=CC=C([O-])C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 17, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 25, 104, 104, 104, 104, 104, 1, 18, 18, 18, 18, 18, 18, 1, 1, 10, 25, 25, 1] 201 rigid atoms, others: [34, 3, 6, 7, 8, 9, 10, 11, 12, 22, 29, 30] set([0, 1, 2, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573555 /scratch/stefan/7901152/working /scratch/stefan/7901152 mkdir: created directory `1' /scratch/stefan/7901152/working/building/REAL300025573555/1 /scratch/stefan/7901152/working/building/REAL300025573555 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/52 `/scratch/stefan/7901152/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC=C(O)C(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025573555.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025573555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573555 none CN(C)S(=O)(=O)C1=CC=C(O)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 200, 201, 93, 93, 93, 93, 93, 39, 38, 38, 8, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 93, 93, 186, 38, 8, 8, 92] 402 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 879 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573555 none CN(C)S(=O)(=O)C1=CC=C(O)C(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 402 conformations in input total number of sets (complete confs): 402 using faster count positions algorithm for large data unique positions, atoms: [18, 8, 18, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 27, 93, 93, 93, 93, 93, 1, 19, 19, 19, 19, 19, 19, 1, 1, 2, 9, 26, 26, 1] 402 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 35, 22, 29, 30] set([0, 1, 2, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573555 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573555 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 1: /scratch/stefan/7901152/working/building/REAL300025573555/1.* 0: /scratch/stefan/7901152/working/building/REAL300025573555/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573555 Building REAL300025573556 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573556' /scratch/stefan/7901152/working/building/REAL300025573556 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573556 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573556/0 /scratch/stefan/7901152/working/building/REAL300025573556 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/53 `/scratch/stefan/7901152/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)C(=O)NCC2=NC(=O)O[N-]2)C=C1Cl) `REAL300025573556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573556 none COC1=CC=C(C(=O)C(=O)NCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 181, 148, 181, 181, 96, 37, 96, 36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 201, 201, 201, 181, 181, 36, 8, 8, 181] 201 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 598 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573556 none COC1=CC=C(C(=O)C(=O)NCC2=NC(=O)O[N-]2)C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 38, 38, 38, 71, 181, 181, 181, 181, 181, 1, 1, 1, 3, 3, 3, 1, 1, 38, 71, 71, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 18, 19, 20, 24, 25, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573556 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573556 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573556/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573556 Building REAL300025573557 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573557' /scratch/stefan/7901152/working/building/REAL300025573557 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573557 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573557/0 /scratch/stefan/7901152/working/building/REAL300025573557 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/54 `/scratch/stefan/7901152/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=CC2=O)C=N1) `REAL300025573557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573557 none CN1C=C(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 1, 7, 7, 7, 28, 144, 144, 144, 144, 144, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 1, 7, 28, 28, 1, 1, 9] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 17, 18, 19, 20, 27, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33]) total number of confs: 244 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573557 none CN1C=C(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 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, 1, 9, 9, 9, 27, 27, 27, 78, 201, 201, 201, 201, 201, 9, 9, 9, 9, 1, 1, 2, 2, 2, 1, 9, 27, 78, 78, 9, 9, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 21, 22, 26] set([5, 6, 7, 8, 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: 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: REAL300025573557 none CN1C=C(N2C=C(C(=O)NCC3=NC(=O)O[N-]3)C=CC2=O)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 11, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 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: [201, 201, 201, 144, 144, 144, 55, 54, 54, 8, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 144, 55, 8, 8, 144, 144, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573557 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573557 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573557/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573557 Building REAL300025573558 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573558' /scratch/stefan/7901152/working/building/REAL300025573558 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573558 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573558/0 /scratch/stefan/7901152/working/building/REAL300025573558 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/55 `/scratch/stefan/7901152/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(F)F)C(C)=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573558 none CC1=NN(CC(F)F)C(C)=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 15, 15, 1, 5, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 198, 201, 201, 103, 103, 33, 32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 103, 103, 103, 198, 198, 201, 103, 103, 103, 32, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 686 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: REAL300025573558 none CC1=NN(CC(F)F)C(C)=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 5, 15, 15, 1, 5, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 17, 17, 1, 1, 1, 1, 9, 9, 9, 21, 103, 103, 103, 103, 103, 2, 2, 2, 5, 5, 17, 2, 2, 2, 9, 21, 21] 201 rigid atoms, others: [0, 1, 2, 3, 4, 8, 9, 10, 11] set([5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 249 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573558 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573558 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573558/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573558 Building REAL300025573559 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573559' /scratch/stefan/7901152/working/building/REAL300025573559 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573559 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573559/0 /scratch/stefan/7901152/working/building/REAL300025573559 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/56 `/scratch/stefan/7901152/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCC2=NC(=O)O[N-]2)C(=O)C2=CC(Cl)=CC=C21) `REAL300025573559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573559 none CCN1C=C(C(=O)NCC2=NC(=O)O[N-]2)C(=O)C2=CC(Cl)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 105, 105, 105, 45, 44, 45, 8, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 105, 182, 182, 182, 182, 182, 105, 44, 8, 8, 105, 105, 105] 182 rigid atoms, others: [8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 669 number of broken/clashed sets: 171 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573559 none CCN1C=C(C(=O)NCC2=NC(=O)O[N-]2)C(=O)C2=CC(Cl)=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 13, 13, 13, 53, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 13, 53, 53, 1, 1, 1] 182 rigid atoms, others: [1, 2, 3, 4, 5, 35, 33, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29] set([0, 32, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 30, 31]) total number of confs: 271 number of broken/clashed sets: 171 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573559 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573559 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573559/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573559 Building REAL300025573560 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573560' /scratch/stefan/7901152/working/building/REAL300025573560 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573560 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573560/0 /scratch/stefan/7901152/working/building/REAL300025573560 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/57 `/scratch/stefan/7901152/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C(C)SC1=CC=CC=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573560 none COC(=O)C(C)SC1=CC=CC=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 164, 201, 144, 164, 78, 78, 78, 78, 78, 78, 22, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 164, 164, 164, 164, 78, 78, 78, 78, 22, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) 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: REAL300025573560 none COC(=O)C(C)SC1=CC=CC=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 17, 24, 8, 17, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 78, 78, 78, 78, 78, 24, 24, 24, 17, 17, 17, 17, 1, 1, 1, 1, 7, 19, 19] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573560 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573560 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573560/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573560 Building REAL300025573561 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573561' /scratch/stefan/7901152/working/building/REAL300025573561 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573561 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573561/0 /scratch/stefan/7901152/working/building/REAL300025573561 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/58 `/scratch/stefan/7901152/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1=NN=C(C2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)O1) `REAL300025573561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573561 none COCCC1=NN=C(C2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 37, 27, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 60, 60, 60, 60, 60, 1, 4, 42, 42, 42, 37, 37, 27, 27, 1, 1, 1, 5, 13, 13, 1] 201 rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573561 none COCCC1=NN=C(C2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 17, 9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 17, 17, 17, 31, 87, 87, 87, 87, 87, 4, 1, 22, 22, 22, 17, 17, 9, 9, 4, 4, 4, 17, 31, 31, 4] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573561 none COCCC1=NN=C(C2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 186, 87, 87, 87, 87, 60, 60, 60, 60, 60, 22, 21, 21, 8, 1, 1, 1, 1, 1, 1, 1, 60, 87, 201, 201, 201, 201, 201, 186, 186, 60, 60, 60, 22, 8, 8, 60] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 733 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573561 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573561 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573561/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573561 Building REAL300025573562 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573562' /scratch/stefan/7901152/working/building/REAL300025573562 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025573562 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573562/0 /scratch/stefan/7901152/working/building/REAL300025573562 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/59 `/scratch/stefan/7901152/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1) `REAL300025573562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573562 none CC1=NC=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 22, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 45, 45, 45, 45, 45, 1, 44, 45, 45, 45, 44, 44, 22, 6, 6, 1, 1, 1, 5, 11, 11, 1] 201 rigid atoms, others: [33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38]) total number of confs: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573562 none CC1=NC=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 18, 44, 44, 44, 44, 44, 103, 103, 103, 117, 201, 201, 201, 201, 201, 44, 1, 2, 2, 2, 1, 1, 4, 18, 18, 44, 44, 44, 103, 117, 117, 44] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573562 none CC1=NC=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 165, 115, 45, 45, 45, 45, 45, 15, 14, 14, 8, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 165, 115, 115, 45, 45, 45, 15, 8, 8, 45] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 643 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573562 /scratch/stefan/7901152/working /scratch/stefan/7901152 mkdir: created directory `1' /scratch/stefan/7901152/working/building/REAL300025573562/1 /scratch/stefan/7901152/working/building/REAL300025573562 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/60 `/scratch/stefan/7901152/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1) `REAL300025573562.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025573562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573562 none CC1=[NH+]C=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 5, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 37, 37, 37, 37, 37, 1, 7, 7, 7, 7, 7, 7, 5, 2, 2, 1, 1, 1, 5, 13, 13, 1] 37 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39]) 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: REAL300025573562 none CC1=[NH+]C=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 21, 37, 37, 37, 37, 37, 7, 1, 2, 2, 2, 1, 1, 4, 7, 7, 7, 7, 7, 7, 21, 21, 7] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573562 none CC1=[NH+]C=CC(NCC2=CC=CC(C(=O)NCC3=NC(=O)O[N-]3)=C2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 31, 31, 31, 8, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 31, 8, 8, 37] 37 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 99 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573562 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573562 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 1: /scratch/stefan/7901152/working/building/REAL300025573562/1.* 0: /scratch/stefan/7901152/working/building/REAL300025573562/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573562 Building REAL300025573563 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573563' /scratch/stefan/7901152/working/building/REAL300025573563 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573563 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573563/0 /scratch/stefan/7901152/working/building/REAL300025573563 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/61 `/scratch/stefan/7901152/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC1=CC(OC)=CC=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573563 none C=CCOC1=CC(OC)=CC=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 186, 109, 60, 60, 60, 29, 60, 97, 60, 60, 27, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 199, 199, 199, 186, 186, 60, 97, 97, 97, 60, 60, 27, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 823 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573563 none C=CCOC1=CC(OC)=CC=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 1, 1, 1, 12, 5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 10, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 8, 8, 8, 16, 60, 60, 60, 60, 60, 74, 74, 74, 37, 37, 1, 3, 3, 3, 1, 1, 8, 16, 16] 201 rigid atoms, others: [32, 3, 4, 5, 6, 7, 9, 10, 11, 12, 27, 31] set([0, 1, 2, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 33, 34, 35]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573563 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573563 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573563/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573563 Building REAL300025573564 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573564' /scratch/stefan/7901152/working/building/REAL300025573564 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573564 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573564/0 /scratch/stefan/7901152/working/building/REAL300025573564 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/62 `/scratch/stefan/7901152/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=CC=N1) `REAL300025573564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573564 none CC(C)(C)OC(=O)NCC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 198, 155, 198, 114, 35, 35, 35, 13, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 35, 35, 19, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 114, 114, 35, 12, 8, 8, 35, 35] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573564 none CC(C)(C)OC(=O)NCC1=CC(C(=O)NCC2=NC(=O)O[N-]2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 39, 39, 38, 22, 38, 8, 1, 1, 1, 1, 1, 5, 5, 5, 9, 35, 35, 35, 35, 35, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 22, 8, 8, 1, 5, 9, 9, 1, 1] 201 rigid atoms, others: [37, 8, 9, 10, 11, 12, 41, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573564 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573564 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573564/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573564 Building REAL300025573565 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573565' /scratch/stefan/7901152/working/building/REAL300025573565 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573565 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573565/0 /scratch/stefan/7901152/working/building/REAL300025573565 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/63 `/scratch/stefan/7901152/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(SC2=CC=CC=C2)=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573565 none CC1=NN(C)C(SC2=CC=CC=C2)=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 6, 1, 1, 1, 1, 1, 1, 1, 17, 17, 64, 64, 64, 96, 201, 201, 201, 201, 201, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 64, 96, 96] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37]) total number of confs: 463 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: REAL300025573565 none CC1=NN(C)C(SC2=CC=CC=C2)=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 17, 17, 7, 17, 17, 1, 1, 12, 12, 12, 34, 117, 117, 117, 117, 117, 2, 2, 2, 2, 2, 2, 17, 17, 7, 17, 17, 12, 34, 34] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 13, 14] set([7, 8, 9, 10, 11, 12, 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: 272 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: REAL300025573565 none CC1=NN(C)C(SC2=CC=CC=C2)=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 14, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 117, 117, 117, 201, 201, 201, 201, 201, 201, 35, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 201, 201, 201, 201, 201, 34, 8, 8] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 330 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573565 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573565 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573565/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573565 Building REAL300025573566 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573566' /scratch/stefan/7901152/working/building/REAL300025573566 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573566 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573566/0 /scratch/stefan/7901152/working/building/REAL300025573566 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/64 `/scratch/stefan/7901152/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1) `REAL300025573566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573566 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 7, 22, 22, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573566 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 8, 1, 1, 1, 1, 1, 1, 1, 26, 96, 96, 96, 46, 96, 96, 96, 185, 201, 201, 201, 201, 25, 8, 8, 96, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 576 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573566 none O=C(NCC1=NC(=O)O[N-]1)C1=CC(Cl)=CC=C1SC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 16, 1, 1, 1, 14, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 24, 66, 66, 104, 201, 201, 201, 201, 201, 24, 24, 24, 24, 24, 24, 7, 1, 1, 1, 1, 1, 1, 66, 104, 104, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28]) total number of confs: 501 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573566 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573566 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573566/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573566 Building REAL300025573567 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573567' /scratch/stefan/7901152/working/building/REAL300025573567 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573567 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573567/0 /scratch/stefan/7901152/working/building/REAL300025573567 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/65 `/scratch/stefan/7901152/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OC2CCOC2)=C1) `REAL300025573567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573567 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OC2CCOC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 21, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 10, 29, 29, 29, 29, 1, 5, 21, 21, 1, 1, 29, 29, 29, 29, 29, 29, 29, 1] 201 rigid atoms, others: [1, 34, 10, 11, 12, 13, 14, 15, 21, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) 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: REAL300025573567 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OC2CCOC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 8, 1, 1, 1, 1, 1, 1, 1, 33, 88, 88, 88, 88, 88, 169, 201, 201, 201, 201, 88, 32, 8, 8, 88, 88, 201, 201, 201, 201, 201, 201, 201, 88] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 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: REAL300025573567 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=NC(OC2CCOC2)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 1, 12, 5, 5, 5, 12, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 29, 81, 81, 126, 201, 201, 201, 201, 201, 29, 29, 29, 29, 6, 1, 1, 1, 1, 1, 1, 29, 81, 126, 126, 29, 29, 1, 1, 1, 1, 1, 1, 1, 28] 201 rigid atoms, others: [32, 33, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 34]) total number of confs: 539 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573567 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573567 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573567/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573567 Building REAL300025573568 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573568' /scratch/stefan/7901152/working/building/REAL300025573568 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573568 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573568/0 /scratch/stefan/7901152/working/building/REAL300025573568 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/66 `/scratch/stefan/7901152/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1=CC=C(C(F)(F)F)C=C1)NCC1=NC(=O)O[N-]1) `REAL300025573568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573568 none O=C(CCCC1=CC=C(C(F)(F)F)C=C1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 32, 106, 123, 184, 201, 201, 184, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 106, 106, 143, 143, 183, 183, 201, 201, 201, 201, 32, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 1029 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573568 none O=C(CCCC1=CC=C(C(F)(F)F)C=C1)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 14, 6, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 67, 67, 95, 201, 201, 201, 201, 201, 14, 14, 6, 6, 4, 4, 1, 1, 1, 1, 67, 95, 95] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573568 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573568 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573568/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573568 Building REAL300025573569 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573569' /scratch/stefan/7901152/working/building/REAL300025573569 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573569 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573569/0 /scratch/stefan/7901152/working/building/REAL300025573569 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/67 `/scratch/stefan/7901152/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(Br)C=C(C(=O)NCC2=NC(=O)O[N-]2)C(=O)N1) `REAL300025573569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573569 none CC1=C(Br)C=C(C(=O)NCC2=NC(=O)O[N-]2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 51, 50, 51, 8, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 50, 8, 8, 78] 78 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 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: REAL300025573569 none CC1=C(Br)C=C(C(=O)NCC2=NC(=O)O[N-]2)C(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'Br', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 11, 8, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 47, 78, 78, 78, 78, 78, 1, 1, 1, 2, 2, 2, 1, 13, 47, 47, 1] 78 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 22, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 23, 24, 25]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573569 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573569 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573569/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573569 Building REAL300025573570 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573570' /scratch/stefan/7901152/working/building/REAL300025573570 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573570 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573570/0 /scratch/stefan/7901152/working/building/REAL300025573570 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/68 `/scratch/stefan/7901152/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H]([N-]C(=O)C(F)(F)F)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573570 none CC(C)[C@H]([N-]C(=O)C(F)(F)F)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.2', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 5, 15, 15, 15, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 88, 127, 31, 88, 88, 159, 193, 193, 193, 193, 193, 30, 31, 8, 1, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 31, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573570 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573570 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573570/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573570 Building REAL300025573571 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573571' /scratch/stefan/7901152/working/building/REAL300025573571 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573571 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573571/0 /scratch/stefan/7901152/working/building/REAL300025573571 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/69 `/scratch/stefan/7901152/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573571 none CCNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 137, 97, 137, 137, 97, 137, 137, 97, 27, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 134, 137, 201, 201, 201, 201, 201, 197, 137, 137, 97, 97, 26, 8, 8, 137, 137] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 1038 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573571 none CCNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 15, 15, 15, 29, 137, 137, 137, 137, 137, 1, 1, 11, 11, 11, 11, 11, 3, 1, 1, 7, 7, 15, 29, 29, 1, 1] 201 rigid atoms, others: [3, 36, 37, 6, 7, 8, 9, 10, 21, 22, 29, 30] set([0, 1, 2, 4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573571 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573571 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573571/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573571 Building REAL300025573572 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573572' /scratch/stefan/7901152/working/building/REAL300025573572 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300025573572 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573572/0 /scratch/stefan/7901152/working/building/REAL300025573572 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/70 `/scratch/stefan/7901152/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1[O-]) `REAL300025573572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573572 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 38, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 10, 38, 38, 1, 1, 1] 63 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573572 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 46, 63, 63, 63, 63, 63, 63, 63, 46, 8, 8, 63, 63, 63] 63 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573572 /scratch/stefan/7901152/working /scratch/stefan/7901152 mkdir: created directory `1' /scratch/stefan/7901152/working/building/REAL300025573572/1 /scratch/stefan/7901152/working/building/REAL300025573572 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/71 `/scratch/stefan/7901152/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1O) `REAL300025573572.mol2' -> `1.mol2' `temp.mol2' -> `REAL300025573572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573572 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 33, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 10, 33, 33, 1, 1, 1, 2] 138 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 24]) total number of confs: 175 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573572 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=CC(I)=C1O NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 18, 1, 12, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 8, 1, 1, 1, 1, 1, 1, 1, 42, 69, 69, 69, 69, 69, 69, 69, 41, 8, 8, 69, 69, 68, 138] 138 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 294 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573572 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573572 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 1: /scratch/stefan/7901152/working/building/REAL300025573572/1.* 0: /scratch/stefan/7901152/working/building/REAL300025573572/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573572 Building REAL300025573573 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573573' /scratch/stefan/7901152/working/building/REAL300025573573 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573573 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573573/0 /scratch/stefan/7901152/working/building/REAL300025573573 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/72 `/scratch/stefan/7901152/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1) `REAL300025573573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573573 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 15, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 57, 57, 57, 57, 7, 15, 15, 1, 1, 1, 25, 25, 57, 57, 57, 57, 57, 57, 57, 57, 57] 201 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573573 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 20, 68, 68, 68, 68, 68, 60, 68, 68, 68, 122, 163, 201, 201, 201, 201, 19, 8, 8, 68, 68, 68, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 631 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573573 none O=C(NCC1=NC(=O)O[N-]1)C1=CC([N+](=O)[O-])=CC=C1SCC1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 8, 11, 11, 1, 1, 1, 14, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 57, 109, 105, 126, 201, 201, 201, 201, 201, 57, 57, 57, 57, 57, 57, 57, 57, 18, 5, 1, 1, 1, 1, 1, 1, 109, 126, 126, 57, 57, 57, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 497 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573573 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573573 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573573/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573573 Building REAL300025573574 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573574' /scratch/stefan/7901152/working/building/REAL300025573574 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573574 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573574/0 /scratch/stefan/7901152/working/building/REAL300025573574 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/73 `/scratch/stefan/7901152/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573574 none CNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 201, 201, 101, 201, 201, 101, 35, 34, 34, 8, 1, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 201, 201, 101, 101, 34, 8, 8, 201, 201] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573574 none CNS(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 7, 15, 15, 15, 47, 201, 201, 201, 201, 201, 1, 1, 5, 5, 5, 5, 1, 1, 7, 7, 15, 47, 47, 1, 1] 201 rigid atoms, others: [33, 2, 5, 6, 7, 8, 9, 34, 20, 21, 26, 27] set([0, 1, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573574 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573574 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573574/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573574 Building REAL300025573575 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573575' /scratch/stefan/7901152/working/building/REAL300025573575 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573575 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573575/0 /scratch/stefan/7901152/working/building/REAL300025573575 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/74 `/scratch/stefan/7901152/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(Br)=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1) `REAL300025573575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573575 none CC1=CC(Br)=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 25, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 24, 8, 8, 63] 63 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 133 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573575 none CC1=CC(Br)=CC(C(=O)NCC2=NC(=O)O[N-]2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 17, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 27, 63, 63, 63, 63, 63, 1, 2, 2, 2, 1, 1, 7, 27, 27, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 17, 21, 22, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 19, 20, 23, 24, 25]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573575 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573575 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573575/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573575 Building REAL300025573576 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573576' /scratch/stefan/7901152/working/building/REAL300025573576 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573576 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573576/0 /scratch/stefan/7901152/working/building/REAL300025573576 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/75 `/scratch/stefan/7901152/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F) `REAL300025573576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573576 none CC(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 42, 42, 42, 107, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 8, 8, 42, 107, 107, 1, 1, 1] 201 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573576 none CC(C(=O)NCC1=NC(=O)O[N-]1)C1=CC=C([N+](=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 8, 11, 11, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 47, 46, 46, 8, 1, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148, 148, 148, 46, 8, 8, 201, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573576 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573576 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573576/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573576 Building REAL300025573577 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573577' /scratch/stefan/7901152/working/building/REAL300025573577 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573577 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573577/0 /scratch/stefan/7901152/working/building/REAL300025573577 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/76 `/scratch/stefan/7901152/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1) `REAL300025573577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573577 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 12, 32, 96, 96, 96, 95, 95, 1, 1, 1, 1, 7, 7, 1, 7, 7, 7, 7, 7, 7, 1, 1, 12, 32, 32, 7, 7, 1, 7, 1, 1] 145 rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 210 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573577 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 8, 1, 1, 1, 1, 1, 1, 1, 46, 96, 96, 96, 145, 145, 103, 145, 145, 145, 145, 145, 145, 96, 96, 45, 8, 8, 145, 145, 96, 145, 96, 95] 145 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573577 none O=C(NCC1=NC(=O)O[N-]1)C1=NN(C2=CC=CC=C2C(F)(F)F)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [37, 7, 37, 37, 76, 145, 145, 145, 145, 145, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 37, 76, 76, 1, 1, 1, 1, 7, 7] 145 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33]) total number of confs: 359 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573577 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573577 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573577/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573577 Building REAL300025573578 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573578' /scratch/stefan/7901152/working/building/REAL300025573578 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573578 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573578/0 /scratch/stefan/7901152/working/building/REAL300025573578 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/77 `/scratch/stefan/7901152/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)C1=CC=C(Cl)C=C1)C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573578 none CC(CC(=O)C1=CC=C(Cl)C=C1)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 26, 78, 124, 186, 186, 201, 201, 201, 201, 201, 201, 25, 26, 8, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 124, 124, 201, 201, 201, 201, 26, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573578 none CC(CC(=O)C1=CC=C(Cl)C=C1)C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 35, 94, 94, 94, 123, 201, 201, 201, 201, 201, 35, 35, 35, 35, 21, 21, 1, 1, 1, 1, 94, 123, 123] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573578 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573578 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573578/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573578 Building REAL300025573579 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573579' /scratch/stefan/7901152/working/building/REAL300025573579 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573579 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573579/0 /scratch/stefan/7901152/working/building/REAL300025573579 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/78 `/scratch/stefan/7901152/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC) `REAL300025573579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573579 none COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 4, 5, 5, 1, 1, 1, 8, 8, 8, 18, 75, 75, 75, 75, 75, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 5, 5, 8, 18, 18, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 17, 18, 19, 37] set([0, 1, 2, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573579 none COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 5, 24, 24, 24, 46, 144, 144, 144, 144, 144, 5, 5, 5, 1, 1, 1, 3, 4, 4, 4, 1, 1, 24, 46, 46, 5, 5, 5, 5, 5, 5, 1, 4, 4, 4] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 20, 21, 22, 27, 28] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573579 none COC1=CC=C(C2(C(=O)NCC3=NC(=O)O[N-]3)CCC2)C=C1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 144, 144, 144, 75, 20, 19, 20, 8, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 144, 144, 144, 201, 201, 201, 201, 144, 144, 19, 8, 8, 75, 75, 75, 75, 75, 75, 144, 201, 201, 201] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573579 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573579 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573579/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573579 Building REAL300025573580 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573580' /scratch/stefan/7901152/working/building/REAL300025573580 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573580 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573580/0 /scratch/stefan/7901152/working/building/REAL300025573580 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/79 `/scratch/stefan/7901152/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC(Cl)=CC2=C1OCC2)NCC1=NC(=O)O[N-]1) `REAL300025573580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573580 none O=C(CC1=CC(Cl)=CC2=C1OCC2)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 30, 109, 201, 201, 201, 200, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 109, 109, 201, 201, 201, 201, 201, 201, 30, 8, 8] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 508 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573580 none O=C(CC1=CC(Cl)=CC2=C1OCC2)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 16, 1, 1, 1, 12, 5, 5, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51, 51, 93, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 51, 93, 93] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 24, 25, 26, 27, 28] set([0, 1, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573580 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573580 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573580/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573580 Building REAL300025573581 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573581' /scratch/stefan/7901152/working/building/REAL300025573581 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573581 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573581/0 /scratch/stefan/7901152/working/building/REAL300025573581 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/80 `/scratch/stefan/7901152/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCSC1=CC=C(Cl)C=C1C(=O)NCC1=NC(=O)O[N-]1) `REAL300025573581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573581 none CCCCSC1=CC=C(Cl)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 176, 115, 73, 73, 73, 24, 73, 73, 71, 24, 23, 23, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 176, 176, 73, 73, 73, 24, 8, 8] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573581 none CCCCSC1=CC=C(Cl)C=C1C(=O)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 1, 1, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 73, 73, 73, 73, 73, 49, 49, 49, 49, 49, 47, 47, 33, 33, 1, 1, 1, 7, 17, 17] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 12, 31] set([0, 1, 2, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573581 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573581 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573581/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573581 Building REAL300025573582 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573582' /scratch/stefan/7901152/working/building/REAL300025573582 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573582 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573582/0 /scratch/stefan/7901152/working/building/REAL300025573582 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/81 `/scratch/stefan/7901152/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=NC=C(Br)C=C1Br) `REAL300025573582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573582 none O=C(NCC1=NC(=O)O[N-]1)C1=NC=C(Br)C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 17, 1, 1, 17, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 1, 1] 53 rigid atoms, others: [1, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573582 none O=C(NCC1=NC(=O)O[N-]1)C1=NC=C(Br)C=C1Br NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 8, 1, 1, 17, 1, 1, 17, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 29, 53, 53, 53, 53, 53, 53, 53, 28, 8, 8, 53, 53] 53 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573582 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573582 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573582/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573582 Building REAL300025573583 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573583' /scratch/stefan/7901152/working/building/REAL300025573583 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573583 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573583/0 /scratch/stefan/7901152/working/building/REAL300025573583 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/82 `/scratch/stefan/7901152/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCC1SCC2NC(=O)NC12)NCC1=NC(=O)O[N-]1) `REAL300025573583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573583 none O=C(CCCCC1SCC2NC(=O)NC12)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 14, 5, 5, 8, 1, 11, 8, 5, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 27, 93, 110, 143, 130, 201, 201, 201, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 1, 93, 93, 128, 128, 146, 139, 148, 148, 201, 201, 201, 201, 201, 201, 201, 26, 8, 8] 201 rigid atoms, others: [16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 989 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: REAL300025573583 none O=C(CCCCC1SCC2NC(=O)NC12)NCC1=NC(=O)O[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 14, 5, 5, 8, 1, 11, 8, 5, 8, 5, 1, 8, 1, 11, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 24, 13, 7, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 107, 201, 201, 201, 201, 201, 24, 24, 13, 13, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 82, 107, 107] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 37, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40]) total number of confs: 533 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573583 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573583 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573583/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573583 Building REAL300025573584 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573584' /scratch/stefan/7901152/working/building/REAL300025573584 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573584 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573584/0 /scratch/stefan/7901152/working/building/REAL300025573584 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/83 `/scratch/stefan/7901152/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1) `REAL300025573584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573584 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 21, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 9, 32, 32, 32, 32, 1, 1, 5, 21, 21, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1] 201 rigid atoms, others: [1, 36, 10, 11, 12, 13, 14, 20, 21, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 232 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573584 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 8, 1, 1, 1, 1, 1, 1, 1, 37, 94, 94, 94, 94, 177, 201, 201, 201, 201, 94, 94, 37, 8, 8, 94, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573584 none O=C(NCC1=NC(=O)O[N-]1)C1=CC=C(OC2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 12, 5, 5, 5, 5, 5, 8, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 32, 82, 82, 128, 201, 201, 201, 201, 201, 32, 32, 32, 7, 1, 1, 1, 1, 1, 1, 32, 32, 82, 128, 128, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32] 201 rigid atoms, others: [32, 33, 34, 35, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 540 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573584 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573584 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573584/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573584 Building REAL300025573585 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573585' /scratch/stefan/7901152/working/building/REAL300025573585 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573585 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573585/0 /scratch/stefan/7901152/working/building/REAL300025573585 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/84 `/scratch/stefan/7901152/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)NCC1(C(=O)NCC2=NC(=O)O[N-]2)CC1) `REAL300025573585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573585 none CC(C)(C)OC(=O)NCC1(C(=O)NCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 173, 194, 130, 65, 21, 20, 21, 8, 1, 1, 1, 1, 1, 1, 1, 65, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 173, 130, 130, 20, 8, 8, 65, 65, 65, 65] 201 rigid atoms, others: [13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 742 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573585 none CC(C)(C)OC(=O)NCC1(C(=O)NCC2=NC(=O)O[N-]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 36, 22, 36, 6, 1, 1, 1, 6, 6, 6, 13, 65, 65, 65, 65, 65, 1, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 22, 6, 6, 6, 13, 13, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 8, 9, 10, 40, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573585 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573585 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573585/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573585 Building REAL300025573586 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573586' /scratch/stefan/7901152/working/building/REAL300025573586 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573586 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573586/0 /scratch/stefan/7901152/working/building/REAL300025573586 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/85 `/scratch/stefan/7901152/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1) `REAL300025573586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573586 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [128, 127, 57, 56, 57, 8, 1, 1, 1, 1, 1, 1, 1, 128, 128, 128, 160, 160, 160, 160, 160, 160, 160, 128, 128, 128, 128, 56, 8, 8, 160, 160, 160] 160 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 323 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573586 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 9, 39, 128, 128, 128, 128, 128, 1, 1, 1, 4, 4, 2, 2, 4, 4, 4, 1, 2, 2, 2, 10, 39, 39, 4, 4, 4] 160 rigid atoms, others: [0, 1, 2, 3, 13, 14, 15, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573586 none CC1=C(C(=O)NCC2=NC(=O)O[N-]2)N=C(C2=CC=C(Cl)C(Cl)=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 8, 1, 1, 1, 1, 1, 16, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 37, 37, 36, 94, 160, 160, 160, 160, 160, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 5, 37, 94, 94, 1, 1, 1] 160 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 463 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573586 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573586 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573586/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573586 Building REAL300025573587 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573587' /scratch/stefan/7901152/working/building/REAL300025573587 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573587 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573587/0 /scratch/stefan/7901152/working/building/REAL300025573587 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/86 `/scratch/stefan/7901152/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)CCCCC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573587 none COC1=CC=C(C(=O)CCCCC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 193, 201, 201, 193, 90, 193, 78, 78, 74, 13, 12, 12, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 90, 90, 78, 78, 78, 78, 74, 74, 12, 8, 8, 201, 201] 201 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573587 none COC1=CC=C(C(=O)CCCCC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 25, 25, 33, 109, 109, 109, 115, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 19, 19, 25, 25, 25, 25, 33, 33, 109, 115, 115, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 41, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 497 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573587 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573587 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573587/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573587 Building REAL300025573588 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573588' /scratch/stefan/7901152/working/building/REAL300025573588 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573588 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573588/0 /scratch/stefan/7901152/working/building/REAL300025573588 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/87 `/scratch/stefan/7901152/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1) `REAL300025573588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573588 none CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 56, 55, 55, 8, 1, 1, 1, 1, 1, 1, 1, 169, 169, 179, 179, 171, 179, 179, 169, 169, 169, 169, 55, 8, 8, 179, 179, 169, 179, 179] 179 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 339 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573588 none CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 55, 169, 169, 169, 169, 169, 1, 1, 6, 6, 1, 6, 6, 1, 2, 2, 2, 13, 55, 55, 6, 6, 1, 6, 6] 179 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 21] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 365 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573588 none CC1=NC(C(=O)NCC2=NC(=O)O[N-]2)=C(C2=CC=CC=C2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 6, 6, 35, 35, 35, 92, 179, 179, 179, 179, 179, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 35, 92, 92, 1, 1, 1, 1, 1] 179 rigid atoms, others: [32, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 470 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573588 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573588 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573588/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573588 Building REAL300025573589 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573589' /scratch/stefan/7901152/working/building/REAL300025573589 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573589 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573589/0 /scratch/stefan/7901152/working/building/REAL300025573589 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/88 `/scratch/stefan/7901152/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573589 none COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 13, 13, 21, 21, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 118, 118, 118, 118, 118, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 10, 22, 22, 21, 21] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573589 none COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 69, 69, 69, 101, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 69, 101, 101, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573589 none COC1=CC=C(C(=O)C2=CC=CC=C2C(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 118, 193, 118, 118, 117, 118, 118, 25, 24, 24, 8, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 118, 118, 118, 118, 24, 8, 8, 201, 201] 201 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573589 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573589 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573589/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573589 Building REAL300025573590 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573590' /scratch/stefan/7901152/working/building/REAL300025573590 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573590 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573590/0 /scratch/stefan/7901152/working/building/REAL300025573590 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/89 `/scratch/stefan/7901152/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCC2=NC(=O)O[N-]2)CC[NH+](CC2=CC=CC=C2)CC1) `REAL300025573590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573590 none CC1(C(=O)NCC2=NC(=O)O[N-]2)CC[NH+](CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 53, 52, 52, 8, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 101, 101, 101, 101, 101, 101, 57, 57, 57, 57, 57, 53, 8, 8, 57, 57, 57, 57, 101, 101, 101, 101, 101, 101, 101, 57, 57, 57, 57] 101 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 370 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: REAL300025573590 none CC1(C(=O)NCC2=NC(=O)O[N-]2)CC[NH+](CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 11, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 7, 9, 9, 8, 9, 9, 1, 1, 2, 2, 2, 3, 11, 11, 1, 1, 1, 1, 7, 7, 9, 9, 9, 9, 9, 1, 1, 1, 1] 101 rigid atoms, others: [0, 1, 2, 34, 33, 32, 44, 42, 43, 12, 13, 14, 15, 16, 23, 24, 45, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 129 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: REAL300025573590 none CC1(C(=O)NCC2=NC(=O)O[N-]2)CC[NH+](CC2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 5, 5, 9, 6, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 17, 17, 17, 37, 101, 101, 101, 101, 101, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 17, 37, 37, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9] 101 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]) total number of confs: 225 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573590 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573590 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573590/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573590 Building REAL300025573591 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573591' /scratch/stefan/7901152/working/building/REAL300025573591 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573591 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573591/0 /scratch/stefan/7901152/working/building/REAL300025573591 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/90 `/scratch/stefan/7901152/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)S(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1) `REAL300025573591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573591 none CC(C)S(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 119, 201, 86, 119, 119, 83, 119, 119, 83, 31, 30, 30, 8, 1, 1, 1, 1, 1, 1, 1, 114, 119, 201, 201, 201, 201, 201, 201, 201, 119, 119, 83, 83, 31, 8, 8, 119, 119] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 1129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573591 none CC(C)S(=O)(=O)C1=CC=C(CC(=O)NCC2=NC(=O)O[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 11, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 34, 119, 119, 119, 119, 119, 1, 1, 7, 7, 7, 7, 7, 7, 7, 1, 1, 6, 6, 15, 34, 34, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 38, 37, 30, 31] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36]) total number of confs: 258 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573591 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573591 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573591/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573591 Building REAL300025573592 mkdir: created directory `/scratch/stefan/7901152/working/building/REAL300025573592' /scratch/stefan/7901152/working/building/REAL300025573592 /scratch/stefan/7901152/working /scratch/stefan/7901152 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300025573592 mkdir: created directory `0' /scratch/stefan/7901152/working/building/REAL300025573592/0 /scratch/stefan/7901152/working/building/REAL300025573592 /scratch/stefan/7901152/working /scratch/stefan/7901152 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7901152/working/3D/91 `/scratch/stefan/7901152/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1) `REAL300025573592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300025573592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7901152/working/building/REAL300025573592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573592 none CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 13, 13, 13, 42, 126, 126, 126, 126, 126, 1, 12, 13, 13, 13, 12, 13, 1, 1, 13, 42, 42] 165 rigid atoms, others: [4, 5, 6, 7, 8, 9, 19, 26, 27] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 28, 29, 30]) total number of confs: 277 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573592 none CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 66, 66, 66, 98, 165, 165, 165, 165, 165, 12, 1, 2, 2, 2, 1, 1, 13, 12, 66, 98, 98] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30]) total number of confs: 434 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300025573592 none CC1=CC=C(C2=CC=C(C(=O)NCC3=NC(=O)O[N-]3)S2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'O.3', 'N.2', 'S.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 8, 1, 11, 12, 8, 14, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 164, 165, 165, 126, 125, 126, 126, 45, 44, 44, 8, 1, 1, 1, 1, 1, 1, 1, 126, 165, 165, 165, 165, 165, 165, 126, 126, 44, 8, 8] 165 rigid atoms, others: [12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 310 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7901152/working/building/REAL300025573592 /scratch/stefan/7901152/working /scratch/stefan/7901152 Finished preparing REAL300025573592 Recording results /scratch/stefan/7901152/working /scratch/stefan/7901152 Appending to /scratch/stefan/7901152/finished/xaaaaax_worked.* 0: /scratch/stefan/7901152/working/building/REAL300025573592/0.* Removing working files in /scratch/stefan/7901152/working/building/REAL300025573592 /scratch/stefan/7901152 Compressing combined databse files /scratch/stefan/7901152/finished/xaaaaax_worked.db2.gz /scratch/stefan/7901152/finished/xaaaaax_worked.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7901152/finished) ======================================================= Finalizing... removed `/scratch/stefan/7901152/working/3D/92' removed directory: `/scratch/stefan/7901152/working/3D' rmdir: removing directory, `/scratch/stefan/7901152/working/building' rmdir: removing directory, `/scratch/stefan/7901152/working' ls: No match. ls: No match.